﻿
@article{ WOS:000826228700001,
Author = {Giordano, Vito and Coli, Elena and Martini, Antonella},
Title = {An Open Data Repository for Engineering Design: Using Text Mining with
   Open Government Data},
Journal = {COMPUTERS IN INDUSTRY},
Year = {2022},
Volume = {142},
Month = {NOV},
Abstract = {Engineering Design (ED) is a complex process in which the reuse of
   knowledge is crucial: applying the knowledge consolidated in previous
   design activities to future design activities means performing them in a
   better way. The relevance of data in ED is even more crucial in a
   business context in which Data Science (DS) is literally revolutionizing
   the way companies operate and therefore also the way data are analyzed.
   Despite having been recognized as crucial for ED processes, data still
   remain closed in the domain and accessible only to their owners due to
   several constraints related to the private and proprietary nature of the
   acquired data. An answer to these challenges could be found in Open
   Data, but at the state of the art an operational Engineering Design
   framework to embrace them is still far to be achieved by both academia
   and industry. Given these issues, the aim of this paper is to give
   evidence that Text Mining can help to make a complex open database more
   effective to be used for the ED process, taking U.S. Open Government
   Data (OGD) repository as a case study. Open access to methods and data
   used within this research is provided. The results of this study allow
   us to understand for which purposes it is possible to apply the datasets
   and to comprehend the expertise and the data science methods needed for
   processing different data for-mats. Moreover, this work opens relevant
   implications and challenges for researchers, practitioners and policy
   makers operating in ED and DS domains that could become opportunities
   for future research and industrial applications. (c) 2022 Elsevier B.V.
   All rights reserved.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Giordano, V (Corresponding Author), Dept Informat Engn, Via Girolamo Caruso 16, I-56122 Pisa, Italy.
   Giordano, Vito; Coli, Elena, Dept Informat Engn, Via Girolamo Caruso 16, I-56122 Pisa, Italy.
   Martini, Antonella, Dept Energy Syst Terr \& Construct Engn, Largo Lucio Lazzarino 2, I-56122 Pisa, Italy.
   Giordano, Vito; Coli, Elena; Martini, Antonella, Business Engn Data Sci B4DS Res Lab, Pisa, Italy.},
DOI = {10.1016/j.compind.2022.103738},
EarlyAccessDate = {JUL 2022},
Article-Number = {103738},
ISSN = {0166-3615},
EISSN = {1872-6194},
Keywords = {Engineering Design; Natural Language Processing; Open Data; Open
   Government Data; Open Data Repository},
Keywords-Plus = {BIG DATA; INNOVATION; BARRIERS; ANALYTICS; EDUCATION},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications},
Author-Email = {vito.giordano@phd.unipi.it},
ResearcherID-Numbers = {COLI, ELENA/ITV-2617-2023
   },
ORCID-Numbers = {COLI, ELENA/0000-0002-2461-6251
   Martini, Antonella/0000-0002-2006-4293},
Number-of-Cited-References = {76},
Times-Cited = {2},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {16},
Journal-ISO = {Comput. Ind.},
Doc-Delivery-Number = {2Y9TA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000826228700001},
DA = {2024-01-15},
}

@article{ WOS:000592826800001,
Author = {Misgar, Safat Mushtaq and Bhat, Ajra and Wani, Zahid Ashraf},
Title = {A study of Open Access research data repositories developed by BRICS
   countries},
Journal = {DIGITAL LIBRARY PERSPECTIVES},
Year = {2021},
Volume = {37},
Number = {1},
Pages = {26-35},
Month = {FEB 6},
Abstract = {Purpose
   In the present era, research data is a concern for researchers, as they
   are trying to find new ways to communicate their research findings and
   conclusions to other researchers in order to increase visibility and
   credibility. BRICS nations are fast emerging economies and contribute
   significantly in research output. This study makes an effort to analyze
   and explore the role of BRICS nations towards open access research data
   repository registered with Registry of Research Data Repositories.
   Design/methodology/approach
   The data were gathered from re3data repository, and the search was
   limited to BRICS nations. The data were further analyzed and tabulated
   as per set parameters, namely, country-wise distribution, types of
   contents, subject coverage and language diversity.
   Findings
   The findings depict that in terms of strength, India has the highest
   number of data repositories, thereby achieved the first rank among BRICS
   nations, and South Africa has the least number of data repositories,
   whereas in terms of content type and subject coverage, India again is
   leading among BRICS nations. The English language is used by
   repositories as the main language of the interface.
   Practical implications
   The study helps to understand the development of research data
   repositories by BRICS nations. The study is further beneficial to
   researchers, as Registry of Research Data Repository provides a single
   platform to access repositories from various disciplines. Readily
   available data saves time, money and efforts of researchers and helps
   the researcher in completing their research activity in a very short
   span of time.
   Originality/value
   The paper has investigated open access data repositories of BRICS nation
   that has not been attempted earlier. This gives readers comprehensive
   overview of research data repositories developed in fast emerging
   economies of the global. The paper can be very helpful for information
   managers, OA promoters and education and research policy makers to
   devise plans and policy bearing in mind the evolving research channels
   in emerging economies.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Wani, ZA (Corresponding Author), Univ Kashmir, Dept Lib \& Informat Sci, Srinagar, India.
   Misgar, Safat Mushtaq; Bhat, Ajra; Wani, Zahid Ashraf, Univ Kashmir, Dept Lib \& Informat Sci, Srinagar, India.},
DOI = {10.1108/DLP-02-2020-0012},
EarlyAccessDate = {NOV 2020},
ISSN = {2059-5816},
EISSN = {2054-1694},
Keywords = {Open access; BRICS; Open data; Research data; Open access research data
   repositories; re3data},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {saffaatmushtaq@gmail.com
   ajrabhat83@gmail.com
   zahidrais@gmail.com},
Affiliations = {University of Kashmir},
ResearcherID-Numbers = {Wani, Zahid A/E-5682-2012},
Number-of-Cited-References = {28},
Times-Cited = {5},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Digit. Libr. Perspect.},
Doc-Delivery-Number = {QK1XM},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000592826800001},
DA = {2024-01-15},
}

@article{ WOS:000370546900004,
Author = {Kitchin, Rob and Collins, Sandra and Frost, Dermot},
Title = {Funding models for Open Access digital data repositories},
Journal = {ONLINE INFORMATION REVIEW},
Year = {2015},
Volume = {39},
Number = {5},
Pages = {664-681},
Abstract = {Purpose - The purpose of this paper is to examine funding models for
   Open Access (OA) digital data repositories whose costs are not wholly
   core funded. Whilst such repositories are free to access, they are not
   without significant cost to build and maintain and the lack of both full
   core costs and a direct funding stream through payment-for-use poses a
   considerable financial challenge, placing their future and the digital
   collections they hold at risk.
   Design/methodology/approach - The authors document 14 different
   potential funding streams for OA digital data repositories, grouped into
   six classes (institutional, philanthropy, research, audience, service,
   volunteer), drawing on the ongoing experiences of seeking a sustainable
   funding for the Digital Repository of Ireland (DRI).
   Findings - There is no straight forward solution to funding OA digital
   data repositories that are not wholly core funded, with a number of
   general and specific challenges facing each repository, and each funding
   model having strengths and weaknesses. The proposed DRI solution is the
   adoption of a blended approach that seeks to ameliorate cyclical effects
   across funding streams by generating income from a number of sources
   rather than overly relying on a single one, though it is still reliant
   on significant state core funding to be viable.
   Practical implications - The detailing of potential funding streams
   offers practical financial solutions to other OA digital data
   repositories which are seeking a means to become financially sustainable
   in the absence of full core funding.
   Originality/value - The review assesses and provides concrete advice
   with respect to potential funding streams in order to help repository
   owners address the financing conundrum they face.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Kitchin, R (Corresponding Author), Natl Univ Ireland Maynooth, Maynooth Univ Social Sci Inst, Maynooth, Kildare, Ireland.
   Kitchin, Rob, Natl Univ Ireland Maynooth, Maynooth Univ Social Sci Inst, Maynooth, Kildare, Ireland.
   Collins, Sandra, Royal Irish Acad, Digital Repository Ireland, Dublin, Ireland.
   Frost, Dermot, Trinity Coll Dublin, Trinity Ctr High Performance Comp, Dublin 2, Ireland.},
DOI = {10.1108/OIR-01-2015-0031},
ISSN = {1468-4527},
EISSN = {1468-4535},
Keywords = {Repositories; Archives; Open Access; Open data; Funding},
Research-Areas = {Computer Science; Information Science \& Library Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Information Science \& Library
   Science},
Author-Email = {Rob.Kitchin@nuim.ie},
Affiliations = {Maynooth University; Royal Irish Academy; Trinity College Dublin},
ResearcherID-Numbers = {Kitchin, Rob/J-8718-2016
   },
ORCID-Numbers = {Kitchin, Rob/0000-0003-4458-7299
   Frost, Dermot/0000-0001-6839-6126},
Funding-Acknowledgement = {Programme for Research in Third-Level Institutions Cycle 5},
Funding-Text = {The research for this paper was funded through the Programme for
   Research in Third-Level Institutions Cycle 5 administered by the Irish
   Higher Education Authority for the Digital Repository of Ireland.},
Number-of-Cited-References = {27},
Times-Cited = {13},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {34},
Journal-ISO = {Online Inf. Rev.},
Doc-Delivery-Number = {DE3RG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000370546900004},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000495667200001,
Author = {Caballero-Rivero, Alejandro and Sanchez-Tarrago, Nancy and Macedo dos
   Santos, Raimundo Nonato},
Title = {Open Science Practices of the Brazilian academic community: A study
   based on scientific production},
Journal = {TRANSINFORMACAO},
Year = {2019},
Volume = {31},
Abstract = {Open Science represents a new approach to scientific work, resulting
   from the fast development of interactive and collaborative modes of
   knowledge acquisition, production, and dissemination facilitated by
   information technologies. The term is used as an ``umbrella{''}
   encompassing a set of initiatives, including Open Access and Open Data.
   This paper, with a scientometric approach, uses the Brazilian scientific
   production of articles published in journals indexed in the Web of
   Science Core Collection during the 2015-2018 period, to investigate the
   practices of the Brazilian academic community related to Open Access and
   Open Data. A stable growth of Open Access articles, representing more
   than a third of the Brazilian scientific production in the Web of
   Science, is observed during that period. Publication in Open Access
   international mega journals is a prominent practice, particularly, in
   the Agriculture and Science \& Technologies research communities, as
   well as the deposit in repositories of previously published articles in
   Open Access journals. Practices related to Open Data still seem
   incipient; the results suggest that the deposit/use of Open Data
   repositories predominates in the areas of Science \& Technology,
   Parasitology and Genetics \& Heredity.},
Publisher = {PONTIFICIA UNIVERSIDADE CATOLICA CAMPINAS},
Address = {NUCLEO EDITORACAO SBI-CCV, CAMPUS II AV JOHN BOYD DUNLOP S-N PREDIO
   ONTOLOGIA JD IPAUSSURAMA, CAMPINAS, SP 13060-904, BRAZIL},
Type = {Article},
Language = {Portuguese},
Affiliation = {Caballero-Rivero, A (Corresponding Author), Univ Fed Pernambuco, Ctr Artes \& Comunicacao, Programa Posgrad Ciencia Informacao, Av Prof Moraes Rego,1235,Cidade Univ, BR-50670901 Recife, PE, Brazil.
   Caballero-Rivero, Alejandro; Macedo dos Santos, Raimundo Nonato, Univ Fed Pernambuco, Ctr Artes \& Comunicacao, Programa Posgrad Ciencia Informacao, Av Prof Moraes Rego,1235,Cidade Univ, BR-50670901 Recife, PE, Brazil.
   Sanchez-Tarrago, Nancy, Univ Fed Rio Grande do Norte, Ctr Ciencias Socials Aplicadas, Dept Ciencia Informacao, Natal, RN, Brazil.},
DOI = {10.1590/2318-0889201931e190029},
Article-Number = {UNSP e190029},
ISSN = {0103-3786},
Keywords = {Open access; Brazil; Open science; Open data; Scientific practices},
Keywords-Plus = {LATIN-AMERICA; OPEN ACCESS},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {caballero.alecaba@gmail.com},
Affiliations = {Universidade Federal de Pernambuco; Universidade Federal do Rio Grande
   do Norte},
ResearcherID-Numbers = {SANTOS, RAIMUNDO NONATO MACEDO DOS/Q-5987-2018
   MACEDO DOS SANTOS, RAIMUNDO NONATO/A-8409-2008
   Sanchez-Tarrago, Nancy/K-2600-2015},
ORCID-Numbers = {MACEDO DOS SANTOS, RAIMUNDO NONATO/0000-0002-9208-3266
   Caballero Rivero, Alejandro/0000-0003-1061-0534
   Sanchez-Tarrago, Nancy/0000-0002-5114-6072},
Number-of-Cited-References = {29},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {28},
Journal-ISO = {Transinformacao},
Doc-Delivery-Number = {JL6VF},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000495667200001},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000427333200005,
Author = {Scotti, Kristen L. and Dunand, David C.},
Title = {Freeze casting - A review of processing, microstructure and properties
   via the open data repository, FreezeCasting.net},
Journal = {PROGRESS IN MATERIALS SCIENCE},
Year = {2018},
Volume = {94},
Pages = {243-305},
Month = {MAY},
Abstract = {Freeze-casting produces materials with complex, three-dimensional pore
   structures which may be tuned during the solidification process. The
   range of potential applications of freeze-cast materials is vast, and
   includes: structural materials, biomaterials, filtration membranes,
   pharmaceuticals, and foodstuffs. Fabrication of materials with
   application specific microstructures is possible via freeze casting,
   however, the templating process is highly complex and the underlying
   principles are only partially understood. Here, we report the creation
   of a freeze-casting experimental data repository, which contains data
   extracted from similar to 800 different freeze-casting papers (as of
   August 2017). These data pertain to variables that link processing
   conditions to microstructural characteristics, and finally, mechanical
   properties. The aim of this work is to facilitate broad dissemination of
   relevant data to freeze-casting researchers, promote better informed
   experimental design, and encourage modeling efforts that relate
   processing conditions to microstructure formation and material
   properties. An initial, systematic analysis of these data is provided
   and key processing-structure-property relationships posited in the
   freeze-casting literature are discussed and tested against the database.
   Tools for data visualization and exploration available through the web
   interface are also provided. (C) 2018 Elsevier Ltd. All rights reserved.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Dunand, DC (Corresponding Author), Northwestern Univ, Dept Mat Sci \& Engn, Evanston, IL 60208 USA.
   Scotti, Kristen L.; Dunand, David C., Northwestern Univ, Dept Mat Sci \& Engn, Evanston, IL 60208 USA.},
DOI = {10.1016/j.pmatsci.2018.01.001},
ISSN = {0079-6425},
EISSN = {1873-2208},
Keywords = {Ice-templating; Solidification; Porous materials; Mechanical properties;
   Data repository},
Keywords-Plus = {POROUS HYDROXYAPATITE SCAFFOLDS; ULTRA-HIGH-POROSITY; INTERCONNECTED
   PORE CHANNELS; CALCIUM-PHOSPHATE SCAFFOLDS; LOW THERMAL-CONDUCTIVITY;
   GLASS 13-93 SCAFFOLDS; X-RAY RADIOGRAPHY; ENHANCED PHOTOCATALYTIC
   PERFORMANCE; STABILIZED ZIRCONIA CERAMICS; ALIGNED MICROPOROUS WALLS},
Research-Areas = {Materials Science},
Web-of-Science-Categories  = {Materials Science, Multidisciplinary},
Author-Email = {dunand@northwestern.edu},
Affiliations = {Northwestern University},
ResearcherID-Numbers = {Dunand, David C/B-7515-2009
   },
ORCID-Numbers = {Dunand, David/0000-0001-5476-7379
   Scotti, Kristen/0000-0002-9529-5213},
Funding-Acknowledgement = {NASA's Physical Sciences Research Program; MaterialsLab Open Science
   Campaign {[}NNH15ZTT002N]; NASA Office of Education and the Science
   Mission Directorate {[}NNH15ZDA010C]; Jack Kent Cooke Foundation},
Funding-Text = {This work was supported by grants from NASA's Physical Sciences Research
   Program, MaterialsLab Open Science Campaign (NNH15ZTT002N) and NASA
   Office of Education and the Science Mission Directorate (NNH15ZDA010C).
   KS was supported by a scholarship through the Jack Kent Cooke
   Foundation. The authors acknowledge Dr. Sylvain Deville (CNRS, France)
   for numerous discussions on the FreezeCasting.net website, database, and
   preparation of this manuscript; the following individuals are also
   acknowledged for their helpful feedback and suggestions on the
   FreezeCasting.net website design: Mr. Jon Chambers (School of the Art
   Institute of Chicago, USA), Mr. Maxime Garnier (ETH, Switzerland), Dr.
   Adam Stevenson (Saint-Gobain, France). The authors acknowledge Mr. Aaron
   Shelhamer (Northern Illinois University, USA) for his assistance with
   the website interactive plotting application.},
Number-of-Cited-References = {893},
Times-Cited = {224},
Usage-Count-Last-180-days = {30},
Usage-Count-Since-2013 = {499},
Journal-ISO = {Prog. Mater. Sci.},
Doc-Delivery-Number = {FZ1JP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000427333200005},
OA = {Green Submitted, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000320497400010,
Author = {Hernandez-Perez, Tony and Garcia-Moreno, Maria-Antonia},
Title = {Open data and data repositories: a new challenge for librarian},
Journal = {PROFESIONAL DE LA INFORMACION},
Year = {2013},
Volume = {22},
Number = {3},
Pages = {259-263},
Month = {MAY-JUN},
Abstract = {The concept of open data, which demands that many more conditions be met
   than simple Internet accessability in any format, is analyzed. Some
   examples are given about the importance of open data repositories in
   efforts to promote transparency in science and avoid scientific fraud.
   Some of the main problems in the management of data repositories are
   discussed.},
Publisher = {EPI},
Address = {APARTADO 32 280, BARCELONA, 08080, SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {Hernández-Pérez, T (Corresponding Author), Univ Carlos III Madrid, Depto Bibliotecon \& Documentac, C Madrid 126, E-28903 Getafe, Madrid, Spain.
   Hernandez-Perez, Tony, Univ Carlos III Madrid, Depto Bibliotecon \& Documentac, E-28903 Getafe, Madrid, Spain.
   Garcia-Moreno, Maria-Antonia, Univ Complutense Madrid, Fac Ciencias Documentac, Madrid 28010, Spain.},
DOI = {10.3145/epi.2013.may.10},
ISSN = {1386-6710},
Keywords = {Open access; Open data; Scientific data; Research data; Data sharing;
   Repositories},
Keywords-Plus = {LINKED-DATA},
Research-Areas = {Communication; Information Science \& Library Science},
Web-of-Science-Categories  = {Communication; Information Science \& Library Science},
Author-Email = {tony@bib.uc3m.es
   mariaant@ccinf.ucm.es},
Affiliations = {Universidad Carlos III de Madrid; Complutense University of Madrid},
ResearcherID-Numbers = {Hernández-Pérez, Tony/K-7800-2013},
ORCID-Numbers = {Hernández-Pérez, Tony/0000-0001-8404-9247},
Number-of-Cited-References = {16},
Times-Cited = {18},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {91},
Journal-ISO = {Prof. Inf.},
Doc-Delivery-Number = {165QC},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000320497400010},
OA = {Green Published, Bronze, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000691830400023,
Author = {Nie, Hua and Luo, Pengcheng and Fu, Ping},
Title = {Research Data Management Implementation at Peking University Library:
   Foster and Promote Open Science and Open Data},
Journal = {DATA INTELLIGENCE},
Year = {2021},
Volume = {3},
Number = {1, SI},
Pages = {189-204},
Month = {WIN},
Abstract = {Research Data Management (RDM) has become increasingly important for
   more and more academic institutions. Using the Peking University Open
   Research Data Repository (PKU-ORDR) project as an example, this paper
   will review a library-based university-wide open research data
   repository project and related RDM services implementation process
   including project kickoff, needs assessment, partnerships establishment,
   software investigation and selection, software customization, as well as
   data curation services and training. Through the review, some issues
   revealed during the stages of the implementation process are also
   discussed and addressed in the paper such as awareness of research data,
   demands from data providers and users, data policies and requirements
   from home institution, requirements from funding agencies and
   publishers, the collaboration between administrative units and
   libraries, and concerns from data providers and users. The significance
   of the study is that the paper shows an example of creating an Open Data
   repository and RDM services for other Chinese academic libraries
   planning to implement their RDM services for their home institutions.
   The authors of the paper have also observed since the PKU-ORDR and RDM
   services implemented in 2015, the Peking University Library (PKUL) has
   helped numerous researchers to support the entire research life cycle
   and enhanced Open Science (OS) practices on campus, as well as impacted
   the national OS movement in China through various national events and
   activities hosted by the PKUL.},
Publisher = {MIT PRESS},
Address = {ONE ROGERS ST, CAMBRIDGE, MA 02142-1209 USA},
Type = {Article},
Language = {English},
Affiliation = {Nie, H (Corresponding Author), Peking Univ Lib, Beijing 100871, Peoples R China.
   Nie, Hua; Luo, Pengcheng, Peking Univ Lib, Beijing 100871, Peoples R China.
   Fu, Ping, Cent Washington Univ Lib, 400 E Univ Way, Ellensburg, WA 98926 USA.},
DOI = {10.1162/dint\_a\_00088},
EISSN = {2641-435X},
Keywords = {Research data management implementation; Open Science; Open Data;
   Research life cycle; Data sharing and reuse},
Keywords-Plus = {ACADEMIC-LIBRARIES; SERVICES; ACCESS},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Author-Email = {hnie@lib.pku.edu.cn
   luopc@lib.pku.edu.cn
   Ping.Fu@cwu.edu},
Affiliations = {Peking University; Central Washington University},
ResearcherID-Numbers = {Fu, Ping/A-2692-2014},
ORCID-Numbers = {Fu, Ping/0000-0002-5386-748X},
Number-of-Cited-References = {28},
Times-Cited = {3},
Usage-Count-Last-180-days = {17},
Usage-Count-Since-2013 = {72},
Journal-ISO = {Data Intell.},
Doc-Delivery-Number = {UK2UP},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000691830400023},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000464050000001,
Author = {Raffaghelli, Juliana E. and Manca, Stefania},
Title = {Is There a Social Life in Open Data? The Case of Open Data Practices in
   Educational Technology Research},
Journal = {PUBLICATIONS},
Year = {2019},
Volume = {7},
Number = {1},
Month = {JAN 28},
Abstract = {In the landscape of Open Science, Open Data (OD) plays a crucial role as
   data are one of the most basic components of research, despite their
   diverse formats across scientific disciplines. Opening up data is a
   recent concern for policy makers and researchers, as the basis for good
   Open Science practices. The common factor underlying these new
   practices-the relevance of promoting Open Data circulation and reuse-is
   mostly a social form of knowledge sharing and construction. However,
   while data sharing is being strongly promoted by policy making and is
   becoming a frequent practice in some disciplinary fields, Open Data
   sharing is much less developed in Social Sciences and in educational
   research. In this study, practices of OD publication and sharing in the
   field of Educational Technology are explored. The aim is to investigate
   Open Data sharing in a selection of Open Data repositories, as well as
   in the academic social network site ResearchGate. The 23 Open Datasets
   selected across five OD platforms were analysed in terms of (a) the
   metrics offered by the platforms and the affordances for social
   activity; (b) the type of OD published; (c) the FAIR (Findability,
   Accessibility, Interoperability, and Reusability) data principles
   compliance; and (d) the extent of presence and related social activity
   on ResearchGate. The results show a very low social activity in the
   platforms and very few correspondences in ResearchGate that highlight a
   limited social life surrounding Open Datasets. Future research
   perspectives as well as limitations of the study are interpreted in the
   discussion.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Raffaghelli, JE (Corresponding Author), Univ Oberta Catalunya, Fac Educ \& Psychol, Barcelona 08018, Spain.
   Raffaghelli, Juliana E., Univ Oberta Catalunya, Fac Educ \& Psychol, Barcelona 08018, Spain.
   Manca, Stefania, Natl Res Council Italy, Inst Educ Technol, I-16149 Genoa, Italy.},
DOI = {10.3390/publications7010009},
Article-Number = {9},
EISSN = {2304-6775},
Keywords = {Open Data; Open Science; Open Data repositories; social media;
   ResearchGate; Educational Technology research},
Keywords-Plus = {DIGITAL SCHOLARSHIP; MEDIA; DECADES; AGE},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {jraffaghelli@uoc.edu
   stefania.manca@itd.cnr.it},
Affiliations = {UOC Universitat Oberta de Catalunya; Consiglio Nazionale delle Ricerche
   (CNR); Istituto per le Tecnologie Didattiche (ITD-CNR)},
ResearcherID-Numbers = {Manca, Stefania/E-5575-2014
   Raffaghelli, Juliana Elisa/S-9024-2016},
ORCID-Numbers = {Manca, Stefania/0000-0002-0348-7139
   Raffaghelli, Juliana Elisa/0000-0002-8753-6478},
Funding-Acknowledgement = {Ministerio de Ciencia e Innovacion {[}RYC-2016-19589]},
Funding-Text = {Ministerio de Ciencia e Innovacion: RYC-2016-19589.},
Number-of-Cited-References = {62},
Times-Cited = {5},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Publications},
Doc-Delivery-Number = {HS7LC},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000464050000001},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000821313900010,
Author = {Wen, Bo and Hu, Paul Jen-Hwa and Ebrahimi, Mohammadreza and Chen,
   Hsinchun},
Title = {Key Factors Affecting User Adoption of Open-Access Data Repositories in
   Intelligence and Security Informatics: An Affordance Perspective},
Journal = {ACM TRANSACTIONS ON MANAGEMENT INFORMATION SYSTEMS},
Year = {2022},
Volume = {13},
Number = {1},
Month = {MAR},
Abstract = {Rich, diverse cybersecurity data are critical for efforts by the
   intelligence and security informatics (ISI) community. Although
   open-access data repositories (OADRs) provide tremendous benefits for
   ISI researchers and practitioners, determinants of their adoption remain
   understudied. Drawing on affordance theory and extant ISI literature,
   this study proposes a factor model to explain how the essential and
   unique affordances of an OADR (i.e., relevance, accessibility, and
   integration) affect individual professionals' intentions to use and
   collaborate with AZSecure, a major OADR. A survey study designed to test
   the model and hypotheses reveals that the effects of affordances on ISI
   professionals' intentions to use and collaborate are mediated by
   perceived usefulness and ease of use, which then jointly determine their
   perceived value. This study advances ISI research by specifying three
   important affordances of OADRs; it also contributes to extant technology
   adoption literature by scrutinizing and affirming the interplay of
   essential user acceptance and value perceptions to explain ISI
   professionals' adoptions of OADRs.},
Publisher = {ASSOC COMPUTING MACHINERY},
Address = {1601 Broadway, 10th Floor, NEW YORK, NY USA},
Type = {Article},
Language = {English},
Affiliation = {Wen, B (Corresponding Author), Univ Utah, David Eccles Sch Business, Dept Operat \& Informat Syst, Salt Lake City, UT 84112 USA.
   Wen, Bo; Hu, Paul Jen-Hwa, Univ Utah, David Eccles Sch Business, Dept Operat \& Informat Syst, Salt Lake City, UT 84112 USA.
   Ebrahimi, Mohammadreza, Univ S Florida, Muma Coll Business, Sch Informat Syst \& Management, Tampa, FL 33620 USA.
   Chen, Hsinchun, Univ Arizona, Dept Management Informat Syst, Tucson, AZ 85721 USA.},
DOI = {10.1145/3460823},
Article-Number = {10},
ISSN = {2158-656X},
EISSN = {2158-6578},
Keywords = {Intelligence and security informatics; open-access data repositories;
   affordance theory; user technology adoption; perceived value; technology
   acceptance},
Keywords-Plus = {PERCEIVED EASE; ACCEPTANCE MODEL; TECHNOLOGY; INTERNET; ANALYTICS;
   QUALITY; VIEW},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Affiliations = {Utah System of Higher Education; University of Utah; State University
   System of Florida; University of South Florida; University of Arizona},
Funding-Acknowledgement = {National Science Foundation {[}ACI-1443019]},
Funding-Text = {This work was partially funded by the National Science Foundation, Data
   Infrastructure Building Blocks (DIBBs) Program, ``CIF21: DIBBs for
   Intelligent and Security Informatics Research and Community,{''} October
   2014 - September 2018, ACI-1443019.},
Number-of-Cited-References = {60},
Times-Cited = {3},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {10},
Journal-ISO = {ACM Trans. Manag. Inf. Syst.},
Doc-Delivery-Number = {2R7UV},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000821313900010},
DA = {2024-01-15},
}

@article{ WOS:001041984400021,
Author = {Kulikov, E. S. and Fedorova, O. S. and Tolmachev, V, I. and Ryazantseva,
   V, U. and Vrazhnov, D. A. and Gubanov, V, A. and Nesterovich, V, S. and
   Shmyrina, A. A.},
Title = {Russian-language open clinical data repository ``SibMED Clinical Data
   Repository{''}},
Journal = {BYULLETEN SIBIRSKOY MEDITSINY},
Year = {2023},
Volume = {22},
Number = {2},
Pages = {182-184},
Abstract = {Global digitalization has become one of the most significant challenges
   in the field of medicine and healthcare. Rapid development of digital
   technologies determines a growing demand for constant access to
   real-time big data. Their use is in need for research and technological
   projects in the field of artificial intelligence technologies. Siberian
   State Medical University developed the first Russian-language clinical
   data repository ``SibMed Clinical Data Repository{''} in Russia
   (https://dataset.ssmu.ru/). The article describes the structure and
   functions of the repository as well as features of its potential use.},
Publisher = {SIBERIAN STATE MEDICAL UNIV},
Address = {UL LENINA 107, TOMSK, 63405, RUSSIA},
Type = {Article},
Language = {English},
Affiliation = {Fedorova, OS (Corresponding Author), Siberian State Med Univ, Intermediate Level Pediat Div, 2 Mos?ow Trakt, Tomsk 634050, Russia.
   Kulikov, E. S.; Nesterovich, S., V, Siberian State Med Univ, 2 Mos?ow Trakt, Tomsk 634050, Russia.
   Fedorova, O. S., Siberian State Med Univ, Intermediate Level Pediat Div, 2 Mos?ow Trakt, Tomsk 634050, Russia.
   Tolmachev, I., V; Vrazhnov, D. A.; Gubanov, A., V, Siberian State Med Univ, Res \& Educ Lab Bion Digital Platforms, 2 Mos?ow Trakt, Tomsk 634050, Russia.
   Ryazantseva, U., V, Siberian State Med Univ, Sci Dept, 2 Mos?ow Trakt, Tomsk 634050, Russia.
   Shmyrina, A. A., Siberian State Med Univ, Dept Digital Technol, 2 Mos?ow Trakt, Tomsk 634050, Russia.},
DOI = {10.20538/1682-0363-2023-2-182-184},
ISSN = {1682-0363},
EISSN = {1819-3684},
Keywords = {open clinical data repository; open data; medical information systems;
   digital health; artificial intelligence; machine learning; open science},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {kulikov.es@ssmu.ru
   dmarkych@gmail.com
   ivantolm@mail.ru
   ryazantseva.uv@ssmu.ru
   vrazhnov.da@ssmu.ru
   derzhiabuz@yandex.ru
   nesterovich.sv@ssmu.ru
   shmyrina.aa@ssmu.ru},
Affiliations = {Siberian State Medical University; Siberian State Medical University;
   Siberian State Medical University; Siberian State Medical University;
   Siberian State Medical University},
ResearcherID-Numbers = {Kulikov, Evgeny/M-6774-2014
   },
ORCID-Numbers = {Kulikov, Evgeny/0000-0002-0088-9204
   Gubanov, Alexander/0000-0001-7465-6238},
Number-of-Cited-References = {10},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {BYULLETEN SIB. MED.},
Doc-Delivery-Number = {O2DU4},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001041984400021},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000864151000004,
Author = {Gonzalez-Vidal, Aurora and Ramallo-Gonzalez, Alfonso P. and Skarmeta,
   Antonio F.},
Title = {Intrinsic and extrinsic quality of data for open data repositories},
Journal = {ICT EXPRESS},
Year = {2022},
Volume = {8},
Number = {3},
Pages = {328-333},
Month = {SEP},
Abstract = {This work assesses the quality of Internet of Things data not only as an
   intrinsic quality on how well it represents the related phenomenon but
   also, on how much information it contains to educate an artificial
   entity. The quality metrics here proposed are tested with real datasets.
   Also, they are implemented on OpenCPU, so the open data repositories can
   use them off-the-shelf to rate their datasets without computational cost
   and minimum human intervention, making them more attractive to potential
   users and gaining visibility and impact. (C) 2022 The Author(s).
   Published by Elsevier B.V. on behalf of The Korean Institute of
   Communications and Information Sciences.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Ramallo-González, AP (Corresponding Author), Univ Murcia, Dept Informat \& Commun Engn, Murcia, Spain.
   Gonzalez-Vidal, Aurora; Ramallo-Gonzalez, Alfonso P.; Skarmeta, Antonio F., Univ Murcia, Dept Informat \& Commun Engn, Murcia, Spain.},
DOI = {10.1016/j.icte.2022.06.001},
EarlyAccessDate = {SEP 2022},
ISSN = {2405-9595},
Keywords = {Data quality; Open data; IoT; Machine learning},
Research-Areas = {Computer Science; Telecommunications},
Web-of-Science-Categories  = {Computer Science, Information Systems; Telecommunications},
Author-Email = {alfonsop.ramallo@um.es},
Affiliations = {University of Murcia},
ResearcherID-Numbers = {Skarmeta Gómez, Antonio/K-4537-2014},
ORCID-Numbers = {Skarmeta Gómez, Antonio/0000-0002-5525-1259},
Funding-Acknowledgement = {EC, Spain {[}893079, 857202]; PRIMA Foundation, Spain; EU, Spain {[}1821
   WATERMED4.0]; Spanish Ministry of Universities, Spain},
Funding-Text = {This work has been sponsored by the EC, Spain through H2020 PHOENIX
   (g.a. 893079), DEMETER (g.a. 857202), Projects and PRIMA Foundation,
   Spain and the EU, Spain g.a. number 1821 WATERMED4.0 -Call 2018 Section
   1 Water. It was also co-financed by the Spanish Ministry of
   Universities, Spain by means of the Margarita Salas linked to the
   European Union through the NextGenerationEU program.},
Number-of-Cited-References = {23},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {ICT Express},
Doc-Delivery-Number = {5C3GD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000864151000004},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000761388200002,
Author = {Redkina, N. S.},
Title = {The Library in the Information Ecosystem of Open Science},
Journal = {SCIENTIFIC AND TECHNICAL INFORMATION PROCESSING},
Year = {2021},
Volume = {48},
Number = {4},
Pages = {239-247},
Month = {OCT},
Abstract = {The results of an analysis of trends in the development of the
   information ecosystem of open science based on the study of the global
   document flow, open access resources, and scientific data repositories,
   as well as initiatives in the field of open science, including during
   the COVID-19 pandemic, are presented. The directions of activity of
   libraries in these conditions are determined.},
Publisher = {PLEIADES PUBLISHING INC},
Address = {PLEIADES HOUSE, 7 W 54 ST, NEW YORK,  NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Redkina, NS (Corresponding Author), Russian Acad Sci, Siberian Branch, State Publ Sci Technol Lib, Novosibirsk, Russia.
   Redkina, N. S., Russian Acad Sci, Siberian Branch, State Publ Sci Technol Lib, Novosibirsk, Russia.},
DOI = {10.3103/S0147688221040043},
ISSN = {0147-6882},
EISSN = {1934-8118},
Keywords = {libraries; open science; information ecosystem; librarian competence;
   open access; repositories; scientific data; information resources},
Keywords-Plus = {ACADEMIC-LIBRARIES},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {redkina@spsl.nsc.ru},
Affiliations = {Russian Academy of Sciences; State Public Scientific \& Technological
   Library of the Siberian Division of the Russian Academy of Sciences},
ResearcherID-Numbers = {Redkina, Natalya/GYE-0913-2022
   Redkina, Natalya S/I-9602-2018},
ORCID-Numbers = {Redkina, Natalya S/0000-0002-3486-9711},
Number-of-Cited-References = {33},
Times-Cited = {4},
Usage-Count-Last-180-days = {19},
Usage-Count-Since-2013 = {73},
Journal-ISO = {Sci. Tech. Inf. Process.},
Doc-Delivery-Number = {ZI1KX},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000761388200002},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:001036210000005,
Author = {Matos, Igor Yure Ramos and Ribeiro Junior, Divino Ignacio and do Prado,
   Jorge Kroll and Argino, Julibio David},
Title = {Overview of scientific production on data repository: copyright and
   thematic representations},
Journal = {ATOZ-NOVAS PRATICAS EM INFORMACAO E CONHECIMENTO},
Year = {2023},
Volume = {12},
Month = {JAN-DEC},
Abstract = {Introduction: this is a survey of scientific production in Information
   Science around research data repositories. Scientific production is
   essential to understand the state of the art and its development over
   the years, especially in emerging themes as proposed here. Research data
   are the main inputs for scientific work in e-Science, concerned with the
   reuse, sharing, collaboration, economy, exchange and speed of research.
   Objective: to present an overview of scientific production in
   Information Science around the topic of research data repositories.
   Method: this is an exploratory, bibliographical and quantitative
   research based on the results found in the following sources of
   information: BRAPCI, SciELO, Portal de Periodicos da CAPES, BDTD and
   Lisa.Results: a total of 127 works published in scientific journals were
   retrieved, with 290 different authors. The literature in English began
   in 2009 to publish data repository reports, and works on metadata and
   data interoperability standards have been retrieved since 2005. It can
   be seen that the first Brazilian article retrieved in the searches is
   from 2015. the year that published the most on the subject, with nine
   articles, against five published in English. Conclusions:: it is an
   emerging topic with increasing production within the CI in Brazil,
   requiring librarians with knowledge and skills to manage repositories
   and research data.},
Publisher = {UNIV FEDERAL PARANA, DEPT CIENCIA \& GESTAO INFORMACAO},
Address = {AV PREFEITO LOTHARIO MEISSNER 632, JARDIM BOTANICO, CURITIBA, PR
   80210-170, BRAZIL},
Type = {Article},
Language = {English},
Affiliation = {Matos, IYR (Corresponding Author), Univ Fed Santa Catarina UFSC, Florianopolis, SC, Brazil.
   Matos, Igor Yure Ramos; Ribeiro Junior, Divino Ignacio; do Prado, Jorge Kroll; Argino, Julibio David, Univ Fed Santa Catarina UFSC, Florianopolis, SC, Brazil.},
DOI = {10.5380/atoz.v12.85255},
Article-Number = {85255},
ISSN = {2237-826X},
Keywords = {Data repositories; Management Research data; Information Science; Open
   access},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {igoryure.rm@gmail.com},
Affiliations = {Universidade Federal de Santa Catarina (UFSC)},
Number-of-Cited-References = {17},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {AtoZ},
Doc-Delivery-Number = {N3QY1},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001036210000005},
DA = {2024-01-15},
}

@article{ WOS:000538520500003,
Author = {Xafis, Vicki and Labude, Markus K.},
Title = {Openness in Big Data and Data Repositories: The Application of an Ethics
   Framework for Big Data in Health and Research},
Journal = {ASIAN BIOETHICS REVIEW},
Year = {2019},
Volume = {11},
Number = {3, SI},
Pages = {255-273},
Month = {SEP},
Abstract = {There is a growing expectation, or even requirement, for researchers to
   deposit a variety of research data in data repositories as a condition
   of funding or publication. This expectation recognizes the enormous
   benefits of data collected and created for research purposes being made
   available for secondary uses, as open science gains increasing support.
   This is particularly so in the context of big data, especially where
   health data is involved. There are, however, also challenges relating to
   the collection, storage, and re-use of research data. This paper gives a
   brief overview of the landscape of data sharing via data repositories
   and discusses some of the key ethical issues raised by the sharing of
   health-related research data, including expectations of privacy and
   confidentiality, the transparency of repository governance structures,
   access restrictions, as well as data ownership and the fair attribution
   of credit. To consider these issues and the values that are pertinent,
   the paper applies the deliberative balancing approach articulated in the
   Ethics Framework for Big Data in Health and Research (Xafis et al. 2019)
   to the domain of Openness in Big Data and Data Repositories. Please
   refer to that article for more information on how this framework is to
   be used, including a full explanation of the key values involved and the
   balancing approach used in the case study at the end.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Xafis, V (Corresponding Author), Natl Univ Singapore, Ctr Biomed Eth, Yong Loo Lin Sch Med, Singapore, Singapore.
   Xafis, Vicki; Labude, Markus K., Natl Univ Singapore, Ctr Biomed Eth, Yong Loo Lin Sch Med, Singapore, Singapore.},
DOI = {10.1007/s41649-019-00097-z},
ISSN = {1793-8759},
EISSN = {1793-9453},
Keywords = {Big data; Open data; Open science; Data repository; Decision-making
   framework; Health data},
Research-Areas = {Social Sciences - Other Topics; Medical Ethics},
Web-of-Science-Categories  = {Ethics; Medical Ethics},
Author-Email = {vicki.xafis@nus.edu.sg},
Affiliations = {National University of Singapore},
ResearcherID-Numbers = {Xafis, Vicki/AAN-9536-2020},
ORCID-Numbers = {Xafis, Vicki/0000-0002-5104-9686},
Funding-Acknowledgement = {Singapore National Medical Research Council Research, Innovation and
   Enterprise 2020 Grant},
Funding-Text = {The development of the Framework and its application to the six Domain
   papers was funded and supported by the Singapore National Medical
   Research Council Research, Innovation and Enterprise 2020 Grant.},
Number-of-Cited-References = {29},
Times-Cited = {13},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Asian Bioeth. Rev.},
Doc-Delivery-Number = {LV6CD},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000538520500003},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000506038800003,
Author = {Bhardwaj, Raj Kumar},
Title = {Open Research Data Repositories: A Content Analysis to Comprehend Data
   Equitable Access},
Journal = {JOURNAL OF SCIENTOMETRIC RESEARCH},
Year = {2019},
Volume = {8},
Number = {3},
Pages = {135-142},
Month = {SEP-DEC},
Abstract = {The present study pertains to content analysis of open Research Data
   Repositories (RDRs) worldwide to comprehend the growth and development
   in the area. The study is original because no attempt has been made so
   far to do a content analysis of these open research data repositories.
   The study used the content analysis method of open RDRs listed on the
   registry of research data repositories. The dataset was analyzed using
   Microsoft Excel. Each unique parameter was given a unique variable for
   the purpose of analysis. Subsequently, the dataset was analyzed using
   Microsoft Excel to achieve the objectives of the study. A simple
   percentage method was followed in analyses and is presented through
   Tables and Figures. The study found that there are 1997 RDRs are open
   worldwide, which are indexed in the registry of research data
   repositories. It was also found that out of these data repositories 1509
   (75.6 percent) are `disciplinary', `institutional' 398 (19.9 percent)
   and `others' 90 (4.5 percent). Majority open RDRs worldwide use the
   World Data System (WDS) certification followed by Core Trust Seal. The
   study found total 70 countries in the world have 1997 RDRs and the
   United States is the leading country with 704 (35.3 percent) open RDRs,
   followed by Germany 201 (10.1 percent), United Kingdom 183 (9.2
   percent), Canada 118 (5.9 percent). Scientific and statistical data
   formats are available in maximum (1238) open research data repositories,
   followed by standard office documents (1108), images (1047), plain text
   (935), raw data (881). It is ascertained that 1049 (52.5) RDRs are not
   following any metadata standard in open RDRs and 948 (47.5 percent)
   follow metadata standards. It was ascertained that Dublin Core is being
   used by (237) data repositories, followed by ISO 19115 (128), Data
   Documentation Initiative (DDI) (125). It was found that 963 (48.2
   percent) data repositories are using unknown and in-house developed
   software worldwide. Majority of research data repositories contains the
   material relating to `Biology' 715 (23.0 percent). Besides this, the
   study found that open data repositories have been developed in 60
   languages worldwide.},
Publisher = {PHCOG NET},
Address = {17, 2ND FLR, BUDDHA VIHAR RD, NEAR SPORTS ZONE, COX TOWN, BENGALURU,
   KARNATAKA, 560005, INDIA},
Type = {Article},
Language = {English},
Affiliation = {Bhardwaj, RK (Corresponding Author), Univ Delhi, St Stephens Coll, Delhi 110007, India.
   Bhardwaj, Raj Kumar, Univ Delhi, St Stephens Coll, Delhi 110007, India.},
DOI = {10.5530/jscires.8.3.29},
ISSN = {2321-6654},
EISSN = {2320-0057},
Keywords = {Research Data; Content Analysis; Data Repository; Researchers; Open Data},
Keywords-Plus = {RESEARCH DATA-MANAGEMENT; DISCOVERY; SCIENCES; METADATA},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {raajchd@gmail.com},
Affiliations = {University of Delhi},
ResearcherID-Numbers = {Bhardwaj, Raj Kumar/J-3482-2016},
ORCID-Numbers = {Bhardwaj, Raj Kumar/0000-0002-0410-1648},
Number-of-Cited-References = {30},
Times-Cited = {1},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {42},
Journal-ISO = {J. Scientometr. Res.},
Doc-Delivery-Number = {KA8GC},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000506038800003},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000565872300001,
Author = {Wilson, Bev and Cong, Cong},
Title = {A Survey of Municipal Open Data Repositories in the U.S.},
Journal = {INTERNATIONAL JOURNAL OF E-PLANNING RESEARCH},
Year = {2020},
Volume = {9},
Number = {4},
Pages = {1-22},
Month = {OCT-DEC},
Abstract = {Cities in the United States are increasingly embracing open data as a
   means of advancing a variety of interests. Promoting transparency,
   facilitating public engagement, proactively managing records requests,
   and fostering innovation in the public and private sectors are among the
   commonly cited motivations for this phenomenon. While there is an
   extensive literature on the benefits and challenges of open government
   data, there are far fewer empirical studies that explore and document
   how these initiatives are unfolding at the local government scale. This
   article asks what kinds of data are being made open in U.S. cities and
   to what extent do open data policies and related regulatory actions
   matter in shaping the content and structure of public-facing
   repositories. The authors conclude that population size and regulatory
   actions exert a positive influence on the amount and variety of datasets
   provided through municipal open data portals. Implications for the
   design and governance of open government data initiatives at the local
   level are also discussed.},
Publisher = {IGI GLOBAL},
Address = {701 E CHOCOLATE AVE, STE 200, HERSHEY, PA 17033-1240 USA},
Type = {Article},
Language = {English},
Affiliation = {Wilson, B (Corresponding Author), Univ Virginia, Urban \& Environm Planning, Sch Architecture, Charlottesville, VA 22903 USA.
   Wilson, Bev, Univ Virginia, Urban \& Environm Planning, Sch Architecture, Charlottesville, VA 22903 USA.
   Cong, Cong, Univ Illinois, Urban \& Reg Planning, Champaign, IL USA.},
DOI = {10.4018/IJEPR.2020100101},
ISSN = {2160-9918},
EISSN = {2160-9926},
Keywords = {Civic Technology; Data Portals; Open Data; Open Government},
Keywords-Plus = {OPEN DATA PORTALS; OPEN GOVERNMENT; QUALITY; CITY},
Research-Areas = {Public Administration},
Web-of-Science-Categories  = {Regional \& Urban Planning},
Affiliations = {University of Virginia; University of Illinois System; University of
   Illinois Urbana-Champaign},
ResearcherID-Numbers = {Cong, Cong/GYR-0073-2022
   },
ORCID-Numbers = {Cong, Cong/0000-0003-1489-4837
   Wilson, Bev/0000-0003-3892-456X},
Number-of-Cited-References = {61},
Times-Cited = {4},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {20},
Journal-ISO = {Int. J. E-Plan. Res.},
Doc-Delivery-Number = {NJ2JT},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000565872300001},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000777901700019,
Author = {Medina Nieto, Maria Auxilio and de la Calleja Mora, Jorge and Zepeda
   Cortes, Claudia and Lopez Dominguez, Eduardo},
Title = {Onto4AIR2: An ontology to manage theses from open repositories},
Journal = {JOURNAL OF INTELLIGENT \& FUZZY SYSTEMS},
Year = {2022},
Volume = {42},
Number = {5},
Pages = {4503-4512},
Abstract = {This paper describes Onto4AIR2, an ontology to manage theses from open
   repositories, this fosters unique and formal definitions of concepts
   from theMexican repositories domain in English and Spanish languages,
   its goal is to support the construction of machine-readable datasets
   that are semantically labeled for further consultations in educational
   organizations. The ontology instances are sample data of theses from the
   National Repository of Mexico, an initiative promoted by the National
   Council of Science and Technology. The paper describes advantages
   derived from the formalisms of the ontology, and describes an assessment
   technique where participants are developers and potential users.
   Developers followed a competency questions-based approach and determined
   that the ontology represents questions and answers using its
   terminology; whereas potential users participated in a satisfaction
   survey; the results showed a positive perception. At present, the level
   of the ontology is proof of concept.},
Publisher = {IOS PRESS},
Address = {NIEUWE HEMWEG 6B, 1013 BG AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Nieto, MAM (Corresponding Author), Polytech Univ Puebla, Postgrad Dept, Puebla, Mexico.
   Medina Nieto, Maria Auxilio; de la Calleja Mora, Jorge, Polytech Univ Puebla, Postgrad Dept, Puebla, Mexico.
   Zepeda Cortes, Claudia, Benemerita Univ Autonoma Puebla, Fac Comp Sci, Puebla, Mexico.
   Lopez Dominguez, Eduardo, Lab Nacl Informat Avanzada LANIA, Dept Comp Sci, Xalapa, Veracruz, Mexico.},
DOI = {10.3233/JIFS-219239},
ISSN = {1064-1246},
EISSN = {1875-8967},
Keywords = {Semantic web; ontologies; machine readable datasets; open data
   repositories; metadata management},
Keywords-Plus = {KNOWLEDGE; DESIGN},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Artificial Intelligence},
Author-Email = {maria.medina@uppuebla.edu.mx},
Affiliations = {Benemerita Universidad Autonoma de Puebla},
Number-of-Cited-References = {40},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {J. Intell. Fuzzy Syst.},
Doc-Delivery-Number = {0G2TB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000777901700019},
DA = {2024-01-15},
}

@article{ WOS:000608009400007,
Author = {Vevera, Adrian-Victor and Barbu, Dragos-Catalin and NEAGU, Gabriel and
   Ciuperca, Ella},
Title = {NI40S-Europe project - support for the National Open Science Cloud
   Initiative},
Journal = {ROMANIAN JOURNAL OF INFORMATION TECHNOLOGY AND AUTOMATIC CONTROL-REVISTA
   ROMANA DE INFORMATICA SI AUTOMATICA},
Year = {2020},
Volume = {30},
Number = {2},
Pages = {81-94},
Abstract = {The mission and vision of the NI4OS-Europe project lies in making a key
   contribution to the European Open Science Cloud (EOSC) service
   portfolio, in the engagement in EOSC governance and in ensuring
   inclusion at European level. To highlight the importance and timeliness
   of these contributions, the paper begins with a presentation of the
   project context by referring to relevant documents adopted at European
   level for the thematic areas of Open Science / Open Data and EOSC. The
   brief presentation of the concepts specific of these areas, and of some
   structures dedicated to their implementation facilitates the detailing
   of the main lines of action of the project which are focused on the
   pre-production infrastructure, services and repositories, and the
   involvement of user communities. The application domains related to
   generic and thematic services, as well as to data repositories are also
   highlighted. The end of the paper is dedicated to the approach of the
   project on the establishment of national OSC initiatives and to the
   presentation of the preliminary results obtained in this respect.},
Publisher = {INST NATL CERCETARE-DEZVOLTARE INFORMATICA-ICI},
Address = {8-10 MARESAL A AVERESCU AV, SECTOR 1, BUCHAREST, 011455, ROMANIA},
Type = {Article},
Language = {Unspecified},
Affiliation = {Vevera, AV (Corresponding Author), Inst Natl Cercetare Dezvoltare Informat ICI Bucur, Bucharest, Romania.
   Vevera, Adrian-Victor; Barbu, Dragos-Catalin; NEAGU, Gabriel; Ciuperca, Ella, Inst Natl Cercetare Dezvoltare Informat ICI Bucur, Bucharest, Romania.
   Barbu, Dragos-Catalin, Acad Studii Econ Bucuresti, Scoala Doctorala Informat Econ, Bucharest, Romania.},
DOI = {10.33436/v30i2y202007},
ISSN = {1220-1758},
EISSN = {1841-4303},
Keywords = {Open Science/Open Data; European Open Science Cloud; NI40S-Europe
   project; the national OSC initiative},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications},
Author-Email = {victor.vevera@ici.ro
   dragos.barbu@ici.ro
   gabriel.neagu@ici.ro
   ella.ciuperca@ici.ro},
Affiliations = {Bucharest University of Economic Studies},
ResearcherID-Numbers = {Barbu, Dragos-Catalin/AAM-3137-2021
   Vevera, Victor Adrian/HLH-0648-2023
   Ciuperca, Ella Magdalena/HKO-1154-2023},
Number-of-Cited-References = {14},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Rom. J. Infor. Tech. Autom. Control},
Doc-Delivery-Number = {PS6BX},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000608009400007},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000424054500002,
Author = {Ogungbeni, John I. and Obiamalu, Amaka R. and Ssemambo, Samuel and
   Bazibu, Charles M.},
Title = {The roles of academic libraries in propagating open science: A
   qualitative literature review},
Journal = {INFORMATION DEVELOPMENT},
Year = {2018},
Volume = {34},
Number = {2},
Pages = {113-121},
Month = {MAR},
Abstract = {This study investigates the roles of academic libraries in propagating
   Open Science. The study is a qualitative survey based on literature
   review. Various definitions of open science from different scholars and
   schools of thought were examined. Research articles on the effects of
   open science on research and the place of academic libraries in
   scientific research were reviewed. Open science enhances collaborations
   and sharing of resources among researchers. Metadata related activities
   are more prevalent due to open science. Open science has increased the
   relevance of science to our environment and world issues like privacy
   and the rightful author of scientific data are still some of the
   challenges facing open science. Academic libraries continue to take
   steps to be involved as key players in the propagation of open science
   through advocacy, building of institutional data repositories and
   serving as hubs for scientific collaboration among others. Academic
   libraries have to do more in the area of advocacy and provision of data
   repositories.},
Publisher = {SAGE PUBLICATIONS LTD},
Address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Ogungbeni, JI (Corresponding Author), Lagos State Univ, Badagry Expressway,PMB 0001,LASU Post Off, Ojo, Lagos State Lag, Nigeria.
   Ogungbeni, John I., Lagos State Univ, Badagry Expressway,PMB 0001,LASU Post Off, Ojo, Lagos State Lag, Nigeria.
   Obiamalu, Amaka R., Nnamdi Azikiwe Univ, Dept Lib \& Informat Sci, Awka, Anambra State, Nigeria.
   Ssemambo, Samuel, Uganda Christian Univ, Dept Lib \& Informat Sci, Mukono, Uganda.
   Bazibu, Charles M., Gulu Univ, Univ Lib, Gulu, Uganda.},
DOI = {10.1177/0266666916678444},
ISSN = {0266-6669},
EISSN = {1741-6469},
Keywords = {academic libraries; open science; open access; open source; scientific
   research; scientific data},
Keywords-Plus = {INSTITUTIONAL REPOSITORIES},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {ogungbeni@gmail.com
   amakaobiamalu@gmail.com
   ssemambosmke@gmail.com
   bazimak@gmail.com},
Affiliations = {Lagos State University},
Number-of-Cited-References = {39},
Times-Cited = {11},
Usage-Count-Last-180-days = {16},
Usage-Count-Since-2013 = {220},
Journal-ISO = {Inf. Dev.},
Doc-Delivery-Number = {FU7TB},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000424054500002},
DA = {2024-01-15},
}

@article{ WOS:001124720500007,
Author = {Zainal, Hazmir and Amanullah, Siti Wahida and Ibrahim, Shamsudin and
   Abdullah, Hendon},
Title = {Cultivating Open Science: a quantitative exploration of leadership
   practices in Malaysian academic libraries},
Journal = {MALAYSIAN JOURNAL OF LIBRARY \& INFORMATION SCIENCE},
Year = {2023},
Volume = {28},
Number = {3},
Pages = {113-128},
Abstract = {This paper explores the characteristics of open leadership to support
   academic library leaders in promoting open science. It also aims to
   identify the existing leadership practices related to the implementation
   of open science from the viewpoint of Malaysian academic library
   leaders. The research employs a quantitative approach, utilizing online
   surveys distributed among 50 leaders from Malaysian public and private
   academic libraries. The study is anchored in the Open Leadership
   Framework, encompassing three key practices: design (contextualization),
   build (structure and system creation), and empower (personal leadership
   skills). Open leadership, viewed as a response to technological
   advancements and the use of multimedia communication tools, is framed
   within the principles, practices, and skills that communities can
   leverage to achieve shared goals. The findings from the design principle
   indicate unanimous agreement among respondents on the importance of
   collaboration, both internally and externally, for the success of the
   open science agenda, aligning with the principles of community
   interactions. In the build principle, all respondents share the belief
   that libraries should implement training and competence development
   programs, aligning with mentoring principles. This adherence corresponds
   to the principles of commons-based production, emphasizing the
   encouragement of publication in open-access journals, and project
   management, highlighting the pivotal role of libraries in determining
   the university's open data repository. In the empowerment principle, a
   total response of 61.5 percent under the ``makes connection{''}
   principle, emphasizes the need for collaboration between the library,
   the university's Information Technology Center, and the Research
   Management Center to provide researcher profiles. This study not only
   provides insights into the current landscape of open leadership
   practices among Malaysian academic library leaders but also offers
   valuable implications for fostering collaboration, training initiatives,
   and empowerment strategies in the realm of open science. By
   understanding and embracing these principles, academic institutions and
   libraries can navigate the evolving scholarly environment, effectively
   contributing to the advancement of open science practices.},
Publisher = {UNIV MALAYA, FAC COMPUTER SCIENCE \& INFORMATION TECH},
Address = {UNIV MALAYA, FAC COMPUTER SCIENCE \& INFORMATION TECH, KUALA LUMPUR,
   50603, MALAYSIA},
Type = {Article},
Language = {English},
Affiliation = {Amanullah, SW (Corresponding Author), Univ Kebangsaan Malaysia, Perpustakaan Tun Seri Lanang, Bangi, Selangor, Malaysia.
   Zainal, Hazmir; Amanullah, Siti Wahida; Ibrahim, Shamsudin; Abdullah, Hendon, Univ Kebangsaan Malaysia, Perpustakaan Tun Seri Lanang, Bangi, Selangor, Malaysia.},
DOI = {10.22452/mjlis.vol28no3.7},
ISSN = {1394-6234},
Keywords = {Open leadership; Library leadership; Open science; Leadership skills;
   Academic libraries},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {hazms@ukm.edu.my
   wydaman@ukm.edu.my
   shamsudin.ibrahim@ukm.edu.my
   hendon.abd@ukm.edu.my},
Affiliations = {Universiti Kebangsaan Malaysia},
Number-of-Cited-References = {41},
Times-Cited = {0},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Malays. J. Libr. Sci.},
Doc-Delivery-Number = {CI8S2},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:001124720500007},
DA = {2024-01-15},
}

@article{ WOS:000346107700005,
Author = {Melero, Remedios and Hernandez-San-Miguel, Javier},
Title = {Open access to research data: a track towards scientific collaboration},
Journal = {REVISTA ESPANOLA DE DOCUMENTACION CIENTIFICA},
Year = {2014},
Volume = {37},
Number = {4},
Abstract = {Knowledge transfer should be facilitated by the opportunities offered by
   information technologies, as they affect the access and distribution of
   digital objects. However barriers to the access and reuse of scholarly
   research, whether economic or copyright-related, inhibit the sharing of
   this valuable common good. The open access movement promotes the
   elimination of these barriers and advocates for an open access culture
   of sharing and reusing materials, while guaranteeing that authors be
   duly acknowledged and that the data be used responsibly. If scientific
   papers have historically been essential for the communication of
   science, in the digital age it is now their building blocks that have
   gained greater importance, especially the observational, descriptive or
   experimental data that underpin the articles. Open research data can be
   reused, transformed by new methods or aggregated to other sources. Open
   access to research data avoids redundancy, provides transparency on how
   they have been obtained and allow for their validation. This work
   provides an overview of some initiatives and recommendations on how to
   share and manage research data and foster open access to it, as a means
   of collaboration between groups or individuals working in similar
   disciplines.},
Publisher = {CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS},
Address = {VITRUVIO 8, 28006 MADRID, SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {Melero, R (Corresponding Author), CSIC, Inst Agroquim \& Tecnol Alimentos, Navarra, Spain.
   Melero, Remedios, CSIC, Inst Agroquim \& Tecnol Alimentos, Navarra, Spain.
   Hernandez-San-Miguel, Javier, Univ Politecn Valencia, Valencia, Spain.},
DOI = {10.3989/redc.2014.4.1154},
Article-Number = {e066},
ISSN = {0210-0614},
Keywords = {Open access; research data; data repositories; data citation; open
   access policies},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {rmelero@iata.csic.es
   frahersa@bib.upv.es},
Affiliations = {Consejo Superior de Investigaciones Cientificas (CSIC); Instituto de
   Agroquimica y Tecnologia de los Alimentos (IATA); Universitat
   Politecnica de Valencia},
ResearcherID-Numbers = {santana, elysmara S D/P-2636-2016
   melero, reme/AAK-3522-2020
   San Miguel, Javier Hernández/H-8441-2014},
ORCID-Numbers = {melero, reme/0000-0002-1813-8783
   San Miguel, Javier Hernández/0000-0001-7276-4964},
Number-of-Cited-References = {33},
Times-Cited = {16},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {70},
Journal-ISO = {Rev. Esp. Doc. Cient.},
Doc-Delivery-Number = {AW2HA},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000346107700005},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001115071400005,
Author = {Mendez, Francisco Javier MARTiNEZ and Baptista, Ana Alice and Carreno,
   Rosana Lopez and Vazquez, Angel Maria Delgado},
Title = {Implementation of research data repositories in Spanish public
   universities: state of the art},
Journal = {SCIRE-REPRESENTACION Y ORGANIZACION DEL CONOCIMIENTO},
Year = {2023},
Volume = {29},
Number = {2},
Pages = {39-49},
Month = {JUL-DEC},
Abstract = {Open Science is gradually making its way into the heart of higher
   education institutions. This paradigm shift aims to make the results of
   scientific research accessible and reusable by other researchers. In
   this regard, open access to research data is particularly important, in
   order to facilitate their reuse and increase their level of
   transparency. Our paper aims to analyse how the deposit of these
   datasets is being carried out in Spanish public universities, their
   level of implementation, which platforms are being implemented and
   whether researchers are being guided and supported in this task. The
   results obtained show a diverse and incipient reality. On the one hand,
   there are two regional consortia of universities (Catalonia and Madrid)
   that are clearly committed to the management of research datasets. On
   the other hand, there is a standard model for depositing this
   information as if they were collections in an institutional repository.
   Universities with more published datasets belong to one of the
   consortia, implement more advanced software and are a model to be
   considered by the others, especially those that have only published a
   few datasets. Support from regional administrations is also a factor to
   consider and an opportunity for communities with several universities.},
Publisher = {UNIV ZARAGOZA},
Address = {C/PEDRO CERBUNA 12, ZARAGOZA, 50009, SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {Méndez, FJM (Corresponding Author), Univ Murcia, Fac Comun \& Documentac, Murcia, Spain.
   Mendez, Francisco Javier MARTiNEZ; Carreno, Rosana Lopez, Univ Murcia, Fac Comun \& Documentac, Murcia, Spain.
   Baptista, Ana Alice, Univ Minho, Escola Engn, Ctr Algoritmi, Minho, Portugal.
   Vazquez, Angel Maria Delgado, Univ Pablo Olavide, Area Bibliotecon \& Documentac, Seville, Spain.},
ISSN = {1135-3716},
EISSN = {2340-7042},
Keywords = {Open science; Research datasets; Research data repositories; Public
   universities; Spain},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {javima@um.es
   analice@dsi.uminho.pt
   rosanalc@um.es
   amdelvaz@gmail.com},
Affiliations = {University of Murcia; Universidade do Minho; Universidad Pablo de
   Olavide},
ResearcherID-Numbers = {Delgado-Vázquez, Ángel M/E-1518-2013},
ORCID-Numbers = {Delgado-Vázquez, Ángel M/0000-0003-2461-8553},
Number-of-Cited-References = {33},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Scire},
Doc-Delivery-Number = {Z9GA2},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001115071400005},
DA = {2024-01-15},
}

@article{ WOS:000585402400001,
Author = {Pavlik, Jan and Hrncirova, Marketa and Stoces, Michal and Masner, Jan
   and Vanek, Jiri},
Title = {Usability of IoT and Open Data Repositories for Analyzing Water
   Pollution. A Case Study in the Czech Republic},
Journal = {ISPRS INTERNATIONAL JOURNAL OF GEO-INFORMATION},
Year = {2020},
Volume = {9},
Number = {10},
Month = {OCT},
Abstract = {Recently, the process of data opening has intensified, especially thanks
   to the involvement of many institutions that have not yet shared their
   data. Some entities provided data to the public long before the trend of
   open data was pushed to a wider level, but many institutions have only
   engaged in this process recently thanks to a systemic state-level effort
   to make data repositories available to the public. Therefore, there are
   many new potential sources of data available for research, including the
   area of water management. This article analyses the current state of
   available data in the Czech Republic-their content, structure, format,
   availability, costs and other indicators that affect the usability of
   these data for independent researchers in the area of water management.
   The case study was conducted to ascertain the levels of accessibility
   and usability of data in open data repositories and the possibilities of
   obtaining data from IoT (Internet of Things) devices such as networked
   sensors where required data is either not available from existing
   sources, too costly, or otherwise unsuitable for the research. The goal
   of the underlying research was to assess the impact/ratio of various
   watershed factors based on monitored indicators of water pollution in a
   model watershed. Such information would help propose measures for
   reducing the volume of pollution resulting in increased security in
   terms of available drinking water for the capital city Prague.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Pavlík, J (Corresponding Author), Czech Univ Life Sci Prague, Dept Informat Technol, Fac Econ \& Management, Kamycka 129, Prague 16500, Czech Republic.
   Pavlik, Jan; Stoces, Michal; Masner, Jan; Vanek, Jiri, Czech Univ Life Sci Prague, Dept Informat Technol, Fac Econ \& Management, Kamycka 129, Prague 16500, Czech Republic.
   Hrncirova, Marketa, ARC Spol Sro, Klimentska 8, Prague 11000, Czech Republic.},
DOI = {10.3390/ijgi9100591},
Article-Number = {591},
EISSN = {2220-9964},
Keywords = {GIS; open data; IoT; diffuse water pollution; spatial data; watershed
   monitoring; factor analysis},
Keywords-Plus = {PHOSPHORUS},
Research-Areas = {Computer Science; Physical Geography; Remote Sensing},
Web-of-Science-Categories  = {Computer Science, Information Systems; Geography, Physical; Remote
   Sensing},
Author-Email = {pavlikjan@pef.czu.cz
   marketa.hrncirova@arcnet.cz
   stoces@pef.czu.cz
   masner@pef.czu.cz
   vanek@pef.czu.cz},
Affiliations = {Czech University of Life Sciences Prague},
ResearcherID-Numbers = {Stočes, Michal/A-6126-2017
   Masner, Jan/B-3683-2017
   Vaněk, Jiří/H-5280-2018
   Pavlík, Jan/T-8397-2017},
ORCID-Numbers = {Stočes, Michal/0000-0001-7128-1071
   Masner, Jan/0000-0003-4593-2306
   Vaněk, Jiří/0000-0002-4573-5348
   Pavlík, Jan/0000-0002-6136-0785},
Funding-Acknowledgement = {Internal grant agency of the Faculty of Economics and Management, Czech
   University of Life Sciences in Prague {[}2019B0009]},
Funding-Text = {This research was funded by Internal grant agency of the Faculty of
   Economics and Management, Czech University of Life Sciences in Prague,
   grant number 2019B0009: ``Life Sciences 4.0{''}.},
Number-of-Cited-References = {23},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {15},
Journal-ISO = {ISPRS Int. Geo-Inf.},
Doc-Delivery-Number = {OL5TP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000585402400001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000668961100012,
Author = {Beauvais, Michael J. S. and Knoppers, Bartha Maria and Illes, Judy},
Title = {A marathon, not a sprint-neuroimaging, Open Science and ethics},
Journal = {NEUROIMAGE},
Year = {2021},
Volume = {236},
Month = {AUG 1},
Abstract = {Open Science is calling for a radical re-thinking of existing scientific
   practices. Within the neuroimaging community, Open Science practices are
   taking the form of open data repositories and open lab notebooks. The
   broad sharing of data that accompanies Open Science, however, raises
   some difficult ethical and legal issues. With neuroethics as a focusing
   lens, we explore eight central concerns posed by open data with regard
   to human brain imaging studies: respect for individuals and communities,
   concern for marginalized communities, consent, privacy protections,
   participatory research designs, contextual integrity, fusions of
   clinical and research goals, and incidental findings. Each consideration
   assists in bringing nuance to the potential benefits for open data
   sharing against associated challenges. We combine current understandings
   with forward-looking solutions to key issues. We conclude by
   underscoring the need for new policy tools to enhance the potential for
   responsible open data.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Beauvais, MJS (Corresponding Author), McGill Univ, Fac Med, Ctr Genom \& Policy, Montreal, PQ, Canada.
   Illes, J (Corresponding Author), Univ British Columbia, Dept Med, Div Neurol, Neuroeth Canada, Vancouver, BC, Canada.
   Beauvais, Michael J. S.; Knoppers, Bartha Maria, McGill Univ, Fac Med, Ctr Genom \& Policy, Montreal, PQ, Canada.
   Illes, Judy, Univ British Columbia, Dept Med, Div Neurol, Neuroeth Canada, Vancouver, BC, Canada.},
DOI = {10.1016/j.neuroimage.2021.118041},
EarlyAccessDate = {APR 2021},
Article-Number = {118041},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords = {Neuroimaging; Neuroethics; Data governance; Open Science; Research
   ethics},
Keywords-Plus = {INCIDENTAL FINDINGS; SOLIDARITY; FRAMEWORK},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {michael.beauvais@mcgill.ca
   jilles@mail.ubc.ca},
Affiliations = {McGill University; University of British Columbia},
ORCID-Numbers = {Beauvais, Michael J. S./0000-0002-8371-3836},
Funding-Acknowledgement = {Canadian Brain Research Strategy (CIHR) {[}171583, 03027 IC127354]},
Funding-Text = {MB is Ethics Officer of the Canadian Open Neuroscience Platform; BMK is
   Canada Research Chair in Law and Medicine and chair of the Canadian Open
   Neuroscience Platform Ethics and Governance Committee; JI is Canada
   Research Chair in Neuroethics, a member of the Canadian Open
   Neuroscience Platform Ethics and Governance Committee, and colead of the
   Canadian Brain Research Strategy (CIHR grant \#171583;03027 IC127354) .
   The authors gratefully acknowledge the insights of reviewers on a
   previous version of this manuscript.},
Number-of-Cited-References = {71},
Times-Cited = {8},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {TC9MI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000668961100012},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000927780100002,
Author = {Zingaro, Marina and Baroni, Carlo and Capolongo, Domenico and
   Mastronuzzi, Giuseppe and Salvatore, Maria Cristina and Scicchitano,
   Giovanni and Vacchi, Matteo},
Title = {OPEN ACCESS DATA REPOSITORY OF LATE-PLEISTOCENE AND HOLOCENE
   PALEO-SHORELINES ALONG THE ANTARCTIC PENINSULA AND SOUTH SHETLAND
   ISLANDS COASTS br},
Journal = {GEOGRAFIA FISICA E DINAMICA QUATERNARIA},
Year = {2021},
Volume = {44},
Number = {2},
Pages = {123-137},
Abstract = {Zingaro M., Baroni C., Capolongo D., Mastro-nuZZi g., salvatore M.C.,
   sCiCChitano g. \& vaCChi M.,Open access data repository of
   Late-Pleistocene and Holocene paleo-shorelines along the Antarctic
   Peninsula and South Shetland Islands coasts. (IT ISSN 0391-9838,
   2021).An improved understanding of the chronology of Antarctic ice sheet
   deglaciation since the Last Glacial Maximum (LGM) represents a
   fundamental tool to better define the origin of past and future
   meltwa-ter influx in the global oceans. Relict shorelines and other
   evidence of past Relative Sea Level (RSL) evolution were widely used to
   understand past ice sheet history and to improve predictions of
   climate-controlled sea level evolution. In the last decades, RSL data in
   the Antarctic region have been mostly produced using a wide range of
   geomorphic evidence such as beach and marine deposits, marine terraces
   and isolation ba-sins. However, the lack of a geographic common
   framework that in-cludes data derived from different sources, limits the
   accessibility to the information. Here we present a new cartographic
   approach to cre-ate an open access geodatabase of the postglacial
   paleo-shorelines by using a standard collecting pattern. Cartographic
   Antarctica Reposito-ry (CAR) includes RSL data along the coasts of the
   Antarctic Peninsula and South Shetland Islands. Results show the
   advantages to use CAR for integrating data and supporting spatial
   analyses, by representing an easy and usable tool for the improvement of
   shoreline evolution defini-tion and the planning of Antarctic coast
   investigations. CAR is dynam-ic repository project that will be further
   expanded on other Antarctic regions too, integrating fully into the wide
   reference context of the free access Antarctic datasets.},
Publisher = {COMITATO GLACIOLOGICO ITALIANO},
Address = {VIA VALPERGA CALUSO 35, TORINO, 10125, ITALY},
Type = {Article},
Language = {English},
Affiliation = {Mastronuzzi, G (Corresponding Author), Univ Bari, Dept Earth \& Geoenvironm Sci, Bari, Italy.
   Mastronuzzi, G (Corresponding Author), Univ Bari, Interdept Res Ctr Coastal Dynam, Bari, Italy.
   Zingaro, Marina; Capolongo, Domenico; Mastronuzzi, Giuseppe; Scicchitano, Giovanni, Univ Bari, Dept Earth \& Geoenvironm Sci, Bari, Italy.
   Baroni, Carlo; Salvatore, Maria Cristina; Vacchi, Matteo, Univ Pisa, Dept Earth Sci, Pisa, Italy.
   Baroni, Carlo; Salvatore, Maria Cristina, Inst Geosci \& Earth Resources, IGG CNR, Pisa, Italy.
   Capolongo, Domenico; Mastronuzzi, Giuseppe; Scicchitano, Giovanni, Univ Bari, Interdept Res Ctr Coastal Dynam, Bari, Italy.},
DOI = {10.4461/GFDQ.2021.44.10},
ISSN = {0391-9838},
EISSN = {1724-4781},
Keywords = {Antarctica; Post-glacial; Paleo-shorelines; Cartographic Repository;
   Open access},
Research-Areas = {Physical Geography},
Web-of-Science-Categories  = {Geography, Physical},
Author-Email = {giuseppe.mastronuzzi@uniba.it},
Affiliations = {Universita degli Studi di Bari Aldo Moro; University of Pisa; Consiglio
   Nazionale delle Ricerche (CNR); Istituto di Geoscienze e Georisorse
   (IGG-CNR); Universita degli Studi di Bari Aldo Moro},
ResearcherID-Numbers = {Baroni, Carlo/D-8184-2012
   Zingaro, Marina/ABE-9795-2020
   Vacchi, Matteo/E-1622-2011},
ORCID-Numbers = {Baroni, Carlo/0000-0001-5905-4650
   Zingaro, Marina/0000-0002-5599-7472
   Vacchi, Matteo/0000-0002-1569-7862},
Number-of-Cited-References = {51},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Geogr. Fis. Din. Quat.},
Doc-Delivery-Number = {VL9NJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000927780100002},
DA = {2024-01-15},
}

@article{ WOS:000479299400007,
Author = {Cho, Jane},
Title = {Study of Asian RDR based on re3data},
Journal = {ELECTRONIC LIBRARY},
Year = {2019},
Volume = {37},
Number = {2},
Pages = {302-313},
Month = {APR 1},
Abstract = {Purpose RDR has become an essential academic infrastructure in an
   atmosphere that facilitates the openness of research output granted by
   public research funds. This study aims to understand operational status
   of 152 Asian data repositories on re3data and cluster repositories into
   four groups according to their operational status. In addition, identify
   the main subject areas of RDRs in Asian countries and try to understand
   what topic correlations exist between data archived in Asian countries.
   Design/methodology/approach This study extracts metadata from re3data
   and analyzes it in various ways to grasp the current status of research
   data repositories in Asian countries. The author clusters the
   repositories into four groups using hierarchical cluster analysis
   according to the level of operation. In addition, for identifying the
   main subject areas of RDRs in Asian countries, extracted the keywords of
   the subject field assigned to the each repository, and Pathfinder
   Network (PFNET) analysis is performed. Findings About 70 per cent of the
   Asian-country repositories are those where licenses or policies are
   declared but not granted permanent identifiers and international-level
   certification. As a result of the subject domain analysis, eight
   clusters are formed centering on life sciences and natural sciences.
   Originality/value The research output in developing countries,
   especially non-English-speaking countries, tends not to be smoothly
   circulated in the international community due to the immaturity of the
   open-access culture, as well as linguistic and technical problems. This
   study has value, in that it investigates the status of Asian countries'
   research data management and global distribution infrastructure in
   global open-science trends.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Cho, J (Corresponding Author), Univ Incheon, Inst Social Sci, Dept Lib \& Informat Sci, Incheon, South Korea.
   Cho, Jane, Univ Incheon, Inst Social Sci, Dept Lib \& Informat Sci, Incheon, South Korea.},
DOI = {10.1108/EL-01-2019-0016},
ISSN = {0264-0473},
EISSN = {1758-616X},
Keywords = {Open access; Asia; Open science; Research data repositories; RDR},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {chojane123@naver.com},
Affiliations = {Incheon National University},
ResearcherID-Numbers = {cho, jane/H-6060-2011},
ORCID-Numbers = {cho, jane/0000-0003-4649-8679},
Number-of-Cited-References = {10},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Electron. Libr.},
Doc-Delivery-Number = {IO3SA},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000479299400007},
DA = {2024-01-15},
}

@article{ WOS:000236054200006,
Author = {Chavan, V and Khadkikar, AS},
Title = {Open access geospatial data repository},
Journal = {CURRENT SCIENCE},
Year = {2006},
Volume = {90},
Number = {5},
Pages = {617-618},
Month = {MAR 10},
Publisher = {CURRENT SCIENCE ASSN},
Address = {C V RAMAN AVENUE, PO BOX 8005, BANGALORE 560 080, INDIA},
Type = {Letter},
Language = {English},
Affiliation = {Chavan, V (Corresponding Author), Informat Div, Natl Chem Lab, Dr Homi Bhabha Rd, Pune 411008, Maharashtra, India.
   Informat Div, Natl Chem Lab, Pune 411008, Maharashtra, India.},
ISSN = {0011-3891},
Keywords-Plus = {GEOGRAPHIC INFORMATION},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {vs.chavan@ncl.res.in},
Affiliations = {Council of Scientific \& Industrial Research (CSIR) - India; CSIR -
   National Chemical Laboratory (NCL)},
ORCID-Numbers = {Chavan, Vishwas/0000-0002-3425-6499},
Number-of-Cited-References = {6},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Curr. Sci.},
Doc-Delivery-Number = {022KH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000236054200006},
DA = {2024-01-15},
}

@article{ WOS:000346109800005,
Author = {Konstantinou, Nikolaos and Spanos, Dimitrios-Emmanuel and Houssos, Nikos
   and Mitrou, Nikolaos},
Title = {Exposing scholarly information as Linked Open Data: RDFizing DSpace
   contents},
Journal = {ELECTRONIC LIBRARY},
Year = {2014},
Volume = {32},
Number = {6},
Pages = {834-851},
Abstract = {Purpose - This paper aims to introduce a transformation engine which can
   be used to convert an existing institutional repository installation
   into a Linked Open Data repository.
   Design/methodology/approach - The authors describe how the data that
   exist in a DSpace repository can be semantically annotated to serve as a
   Semantic Web (meta)data repository.
   Findings - The authors present a non-intrusive, standards-compliant
   approach that can run alongside with current practices, while
   incorporating state-of-the art methodologies.
   Originality/value - Also, they propose a set of mappings between domain
   vocabularies that can be (re)used towards this goal, thus offering an
   approach that covers both the technical and semantic aspects of the
   procedure.},
Publisher = {EMERALD GROUP PUBLISHING LIMITED},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Konstantinou, N (Corresponding Author), Natl Hellen Res Fnd, Natl Documentat Ctr, Athens, Greece.
   Konstantinou, Nikolaos; Houssos, Nikos, Natl Hellen Res Fnd, Natl Documentat Ctr, Athens, Greece.
   Spanos, Dimitrios-Emmanuel; Mitrou, Nikolaos, Natl Tech Univ Athens, Sch Elect \& Comp Engn, Athens, Greece.},
DOI = {10.1108/EL-12-2012-0156},
ISSN = {0264-0473},
EISSN = {1758-616X},
Keywords = {Semantic Web; Linked Open Data; Mapping; DSpace; Relational database;
   Ontology},
Keywords-Plus = {WEB},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {nkons@ekt.gr},
Affiliations = {National Hellenic Research Foundation; National Technical University of
   Athens},
ResearcherID-Numbers = {Spanos, Dimitrios-Emmanuel/H-6437-2019
   Houssos, Nikos/AAO-4620-2021
   Konstantinou, Nikolaos/J-4676-2014},
ORCID-Numbers = {Spanos, Dimitrios-Emmanuel/0000-0001-9446-9499
   Houssos, Nikos/0000-0002-5277-285X
   Konstantinou, Nikolaos/0000-0003-3742-9276},
Number-of-Cited-References = {22},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {23},
Journal-ISO = {Electron. Libr.},
Doc-Delivery-Number = {AW2HW},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000346109800005},
DA = {2024-01-15},
}

@article{ WOS:001057877200002,
Author = {Pampel, Heinz and Weisweiler, Nina Leonie and Strecker, Dorothea and
   Witt, Michael and Vierkant, Paul and Elger, Kirsten and Bertelmann,
   Roland and Buys, Matthew and Ferguson, Lea Maria and Kindling, Maxi and
   Kotarski, Rachael and Petras, Vivien},
Title = {re3data-Indexing the Global Research Data Repository Landscape Since
   2012},
Journal = {SCIENTIFIC DATA},
Year = {2023},
Volume = {10},
Number = {1},
Month = {AUG 29},
Abstract = {For more than ten years, re3data, a global registry of research data
   repositories (RDRs), has been helping scientists, funding agencies,
   libraries, and data centers with finding, identifying, and referencing
   RDRs. As the world's largest directory of RDRs, re3data currently
   describes over 3,000 RDRs on the basis of a comprehensive metadata
   schema. The service allows searching for RDRs of any type and from all
   disciplines, and users can filter results based on a wide range of
   characteristics. The re3data RDR descriptions are available as Open Data
   accessible through an API and are utilized by numerous Open Science
   services. re3data is engaged in various initiatives and projects
   concerning data management and is mentioned in the policies of many
   scientific institutions, funding organizations, and publishers. This
   article reflects on the ten-year experience of running re3data and
   discusses ten key issues related to the management of an Open Science
   service that caters to RDRs worldwide.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Pampel, H (Corresponding Author), Humboldt Univ, Berlin Sch Lib \& Informat Sci, Berlin, Germany.
   Pampel, H; Weisweiler, NL (Corresponding Author), Helmholtz Open Sci Off, Helmholtz Assoc, Potsdam, Germany.
   Pampel, Heinz; Strecker, Dorothea; Petras, Vivien, Humboldt Univ, Berlin Sch Lib \& Informat Sci, Berlin, Germany.
   Pampel, Heinz; Weisweiler, Nina Leonie; Bertelmann, Roland; Ferguson, Lea Maria, Helmholtz Open Sci Off, Helmholtz Assoc, Potsdam, Germany.
   Witt, Michael, Univ Purdue, Distributed Data Curat Ctr, W Lafayette, IN USA.
   Vierkant, Paul; Buys, Matthew, DataCite Int Data C Initiat e V, Hannover, Germany.
   Elger, Kirsten, GFZ German Res Ctr Geosci, Lib \& Informat Serv, Potsdam, Germany.
   Kindling, Maxi, Free Univ Berlin, Open Access Buro Berlin, Berlin, Germany.
   Kotarski, Rachael, Univ Bath, Lib, Bath, England.},
DOI = {10.1038/s41597-023-02462-y},
Article-Number = {571},
EISSN = {2052-4463},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {heinz.pampel@hu-berlin.de
   nina.weisweiler@os.helmholtz.de},
Affiliations = {Humboldt University of Berlin; Helmholtz Association; Helmholtz
   Association; Helmholtz-Center Potsdam GFZ German Research Center for
   Geosciences; Free University of Berlin; University of Bath},
ResearcherID-Numbers = {Pampel, Heinz/J-5635-2014
   Bertelmann, Roland/C-4211-2012
   },
ORCID-Numbers = {Strecker, Dorothea/0000-0002-9754-3807
   Elger, Kirsten/0000-0001-5140-8602
   Weisweiler, Nina Leonie/0000-0001-6967-9443
   Pampel, Heinz/0000-0003-3334-2771
   Bertelmann, Roland/0000-0002-5588-0290
   Kotarski, Rachael/0000-0001-6843-7960},
Funding-Acknowledgement = {German Research Foundation (DFG) {[}422587133, 491192747]; Community
   Building, Networking and Research Data Management Services; Deutsche
   Forschungsgemeinschaft (DFG, German Research Foundation); Open Access
   Publication Fund of Humboldt-Universitaet zu Berlin;  {[}209240528]},
Funding-Text = {This work has been supported by the German Research Foundation (DFG)
   under the projects <EM>re3data.org - Registry of Research Data
   Repositories. Community Building, Networking and Research Data
   Management Services</EM> (Grant ID: 209240528) and <EM>re3data</EM> -
   <EM>Offene und nutzerorientierte Referenz fuer
   Forschungsdatenrepositorien (re3data COREF)</EM> (Grant ID:
   422587133).\& nbsp;The article processing charge was funded by the
   Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) -
   491192747 and the Open Access Publication Fund of Humboldt-Universitaet
   zu Berlin.},
Number-of-Cited-References = {97},
Times-Cited = {1},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Sci. Data},
Doc-Delivery-Number = {Q5JH6},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001057877200002},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000943230500001,
Author = {Moradi, Sh and Abdi, S.},
Title = {Open science-related policies in Europe},
Journal = {SCIENCE AND PUBLIC POLICY},
Year = {2023},
Volume = {50},
Number = {3},
Pages = {521-530},
Month = {JUN 15},
Abstract = {This study aims to review the open science (OS) policy documents,
   identify their subject areas, and distinguish the topics of OS support
   policies in seven European countries, providing a platform for practical
   cooperation between countries in science popularization. With a
   qualitative-inductive approach, all pertinent policy documents in OS
   were collected through documentary study, and thematic analysis was
   conducted to identify OS policies for each country. Finally, forty-six
   policy documents extracted up to December 2020 were thematically
   analyzed through a qualitative-inductive case study. All selected
   countries had developed OS policies, and these supportive policies were
   generally related to the three dimensions of `open input, open process,
   and open output'. In `open input', recommendations for the performance
   of research data repositories, as well as management criteria, are
   considered. Most countries adopted `open output' protectionist policies.
   Multiple policies in the `open process' indicate the need for an
   appropriate OS platform.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Moradi, S (Corresponding Author), Univ St Augustine Hlth Sci, Lib, 700 Windy Point Dr, San Marcos, CA 92069 USA.
   Moradi, Sh, Univ St Augustine Hlth Sci, Lib, 700 Windy Point Dr, San Marcos, CA 92069 USA.
   Abdi, S., Natl Res Inst Sci Policy NRISP, Policy Evaluat \& Sci Technol \& Innovat Monitoring, Tehran, Iran.},
DOI = {10.1093/scipol/scac082},
EarlyAccessDate = {MAR 2023},
ISSN = {0302-3427},
EISSN = {1471-5430},
Keywords = {open scholarship; open access; open data; open scholarly communication;
   open scientific communication; European countries; policy assessment},
Research-Areas = {Environmental Sciences \& Ecology; Business \& Economics; Public
   Administration},
Web-of-Science-Categories  = {Environmental Studies; Management; Public Administration},
Author-Email = {smoradi@usa.edu},
ResearcherID-Numbers = {Moradi, Shima/M-7021-2016},
ORCID-Numbers = {Moradi, Shima/0000-0001-5556-4098},
Number-of-Cited-References = {40},
Times-Cited = {0},
Usage-Count-Last-180-days = {12},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Sci. Public Policy},
Doc-Delivery-Number = {I8GQ0},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000943230500001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000645554900001,
Author = {Kim, Youngseek},
Title = {A study of the determinants of psychologists' data sharing and open data
   badge adoption},
Journal = {LEARNED PUBLISHING},
Year = {2021},
Volume = {34},
Number = {4},
Pages = {499-509},
Month = {OCT},
Abstract = {This research examines whether attitudinal, normative, and behavioural
   control factors affect psychologists' data sharing and open data badge
   adoption intentions. The results from the multivariate regression
   demonstrate that psychologists' (n = 338) data sharing and open data
   badge adoption intentions are commonly influenced by perceived community
   benefit, norm of data sharing, and perceived effort involved to share
   datasets. Additionally, psychologists' data sharing intentions are
   affected by additional, normative, and control factors including the
   norm of reciprocity, IRB requirements, and availability of data
   repositories. As it concerns open data badge adoption, psychologists are
   affected by additional attitudinal factors, including perceived academic
   reputation and risk. This research suggests psychologists' motivations
   to share data and for open data badge adoption differ, so different
   strategies are needed to better promote psychologists' data sharing and
   open data badge adoption.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Kim, Y (Corresponding Author), Sungkyunkwan Univ, Dept Lib \& Informat Sci, 25-2 Sungkyunkwan Ro, Seoul 03063, South Korea.
   Kim, Youngseek, Sungkyunkwan Univ, Dept Lib \& Informat Sci, 25-2 Sungkyunkwan Ro, Seoul 03063, South Korea.},
DOI = {10.1002/leap.1388},
EarlyAccessDate = {APR 2021},
ISSN = {0953-1513},
EISSN = {1741-4857},
Keywords = {data reuse; data sharing; open data badge; open science; psychology},
Keywords-Plus = {DATA CURATION; KNOWLEDGE; COMMUNICATION; REPOSITORIES; BEHAVIORS;
   SCIENCES; METADATA; ROLES},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {youngseekkim@skku.edu},
Affiliations = {Sungkyunkwan University (SKKU)},
Number-of-Cited-References = {47},
Times-Cited = {2},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {42},
Journal-ISO = {Learn. Publ.},
Doc-Delivery-Number = {WB9JL},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000645554900001},
DA = {2024-01-15},
}

@article{ WOS:000975248300002,
Author = {Astsatryan, Hrachya and Lalayan, Arthur},
Title = {SCALABLE DATA PROCESSING PLATFORM FOR EARTH OBSERVATION DATA
   REPOSITORIES},
Journal = {SCALABLE COMPUTING-PRACTICE AND EXPERIENCE},
Year = {2023},
Volume = {24},
Number = {1},
Pages = {35-44},
Month = {MAR},
Abstract = {Earth observation (EO) satellite data is essential to environmental
   monitoring. At a national and regional level, the open data cubes
   harness the power of satellite data by providing application programming
   interfaces and services to the end-users. The volume and the complexity
   of satellite observations are increasing, demanding novel approaches for
   data storing, managing, and processing. High-performance computing (HPC)
   and cloud platforms may improve Big EO data processing performance.
   However, it is necessary to consider several vital aspects for efficient
   and flexible EO data processing, such as the interoperability from
   cloud-HPC and EO data repositories, automatic provisioning and scaling
   of cloud-HPC resources, cost-effectiveness, support of new EO data
   formats and open-source packages, or linkage with data cube platforms.
   The article proposes a scalable EO data processing platform
   interoperable from cloud-HPC and EO data repositories. The platform
   enables linking any data repository supporting web coverage service or
   SpatioTemporal Asset Catalog Application Programming Interfaces
   (STAC-API), and any cloud or HPC resource supporting scheduling system
   API for providing access to the cluster backends.},
Publisher = {UNIV VEST TIMISOARA, WEST UNIV TIMISOARA},
Address = {BLVD VASILE PARVAN 4, TIMISOARA, TIMIS 300223, ROMANIA},
Type = {Article},
Language = {English},
Affiliation = {Astsatryan, H (Corresponding Author), Univ Geneva, Gregory GiulianiInst Environm Sci, CH-1205 Geneva, Switzerland.
   Astsatryan, Hrachya; Lalayan, Arthur, Natl Acad Sci Armenia, Inst Informat \& Automat Problems, 1 Paruyr Sevak Str, Yerevan 0014, Armenia.
   Astsatryan, Hrachya, Univ Geneva, Gregory GiulianiInst Environm Sci, CH-1205 Geneva, Switzerland.},
DOI = {10.12694/scpe.v24i1.2041},
ISSN = {1895-1767},
Keywords = {Earth observation satellite data; cloud and HPC; DataCube; STAC; COG;
   Dask},
Keywords-Plus = {ANALYSIS READY DATA; OPEN DATA CUBE},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Software Engineering},
Author-Email = {hrach@sci.am
   arthurlalayan97@gmail.com},
Affiliations = {National Academy of Sciences of Armenia; Institute for Informatics \&
   Automation Problems (IIAP) - NAS RA; University of Geneva},
ResearcherID-Numbers = {Astsatryan, Hrachya/D-8069-2013},
ORCID-Numbers = {Astsatryan, Hrachya/0000-0001-8872-6620},
Funding-Acknowledgement = {University of Geneva Leading House; State Committee of Science of the
   Republic of Armenia {[}21AG-1B052, 21SC-BRFFR-1B009]},
Funding-Text = {The research was supported by the University of Geneva Leading House and
   the State Committee of Science of the Republic of Armenia by the
   projects entitled ``ADC4SD: Armenian Data Cube for Sustainable
   Development{''}, ``Self-organized Swarm of UAVs Smart cloud Platform
   Equipped with Multi-agent Algorithms and Systems{''} (Nr. 21AG-1B052)
   and ``Remote sensing data processing methods using neural networks and
   deep learning to predict changes in weather phenomena{''} (Nr.
   21SC-BRFFR-1B009).},
Number-of-Cited-References = {30},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Scalable Comput.-Pract. Exp.},
Doc-Delivery-Number = {E4KN2},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000975248300002},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000459208000002,
Author = {Kim, Jihyun},
Title = {Overview of disciplinary data sharing practices and promotion of open
   data in science},
Journal = {SCIENCE EDITING},
Year = {2019},
Volume = {6},
Number = {1},
Pages = {3-9},
Month = {FEB},
Abstract = {The present study specifies the historical development of data sharing
   practices in three disciplines-oceanography, ecology, and genomics-along
   with the evolving progress of movements-e-Science, cyberinfrastructure,
   and open science-that expedite data sharing in more diverse disciplines.
   The review of these disciplinary data-sharing practices and the
   movements suggests opportunities and challenges that would serve as a
   basis for implementing data-sharing practices. The increasing need for
   large-scale and interdisciplinary research provides momentum for
   initiating data sharing. In addition, the development of data
   repositories and standards for metadata and data format facilitates data
   sharing. However, challenges need to be addressed, in regard to
   conflicting issues of patenting data, concerns about privacy and
   confidentiality, and informed consent that adequately enables data
   sharing. It is also necessary to consider the needs of the various
   stakeholders involved in data sharing to incentivize them to improve its
   impact.},
Publisher = {KOREAN COUNCIL SCIENCE EDITORS},
Address = {KOREA SCIENCE \& TECHNOLOGY CENTER 2ND FL, 22 TEHERAN-RO 7-GIL,
   GANGNAM-GU, SEOUL, 06130, SOUTH KOREA},
Type = {Review},
Language = {English},
Affiliation = {Kim, J (Corresponding Author), Ewha Womans Univ, Dept Lib \& Informat Sci, Seoul, South Korea.
   Kim, Jihyun, Ewha Womans Univ, Dept Lib \& Informat Sci, Seoul, South Korea.},
DOI = {10.6087/kcse.149},
ISSN = {2288-7474},
EISSN = {2288-8063},
Keywords = {Data sharing; Disciplinary data sharing practices; Movements for open
   data; Open data; Open science},
Research-Areas = {Communication},
Web-of-Science-Categories  = {Communication},
Author-Email = {kim.jh@ewha.ac.kr},
Affiliations = {Ewha Womans University},
ORCID-Numbers = {Kim, Jihyun/0000-0003-0209-4365},
Number-of-Cited-References = {21},
Times-Cited = {8},
Usage-Count-Last-180-days = {12},
Usage-Count-Since-2013 = {40},
Journal-ISO = {Sci. Ed.},
Doc-Delivery-Number = {HM1JU},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000459208000002},
OA = {gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000886088500022,
Author = {Rudolph, Elizabeth M. and Hedding, David W. and De Bruyn, P. J. Nico and
   Nel, Werner},
Title = {An open access geospatial database for the sub-Antarctic Prince Edward
   Islands},
Journal = {SOUTH AFRICAN JOURNAL OF SCIENCE},
Year = {2022},
Volume = {118},
Number = {9-10},
Month = {SEP-OCT},
Abstract = {Researchers of projects at the sub-Antarctic Prince Edward Islands are
   increasingly considering geospatial data as an essential component in
   answering scientific questions. A need exists for high-resolution
   geospatial data in both multi- and transdisciplinary research to better
   analyse fine-scale biotic-abiotic interactions of the Islands' landscape
   and ecosystems within the context of climate change and the impacts of
   invasive species. However, much of the geospatial data that currently
   exist have limitations in spatial coverage and/or resolution, are
   outdated, or are not readily available. To address these issues, we
   present an online geospatial database for the Prince Edward Islands
   (both islands) produced from a high-resolution digital surface model and
   satellite imagery. This database contains vector files, raster data
   sets, and maps of topographical and hydrological parameters. It is
   freely available to download from Figshare - an open access data
   repository. We encourage the South African polar science community to
   make use of similar platforms for improved data sharing practices.
   Significance:
   A topographical and hydrological geospatial database - produced from a 1
   m x 1 m digital surface model of the Prince Edward Islands - is
   provided.
   These fine-scale geospatial data allow for a more comprehensive
   assessment of biotic-abiotic interactions at an island scale.
   Also included are locality maps specifying place names and established
   long-term marine mammal monitoring beaches and coastal zones for
   improved cross-referencing.
   The dataset is downloadable from an open access data repository and
   intended to promote open science and data sharing practices.},
Publisher = {ACAD SCIENCE SOUTH AFRICA A S S AF},
Address = {PO BOX 72135, LYNWOOD RIDGE 0040, SOUTH AFRICA},
Type = {Article},
Language = {English},
Affiliation = {Rudolph, EM (Corresponding Author), Univ Free State, Afromontane Res Unit, Dept Geog, Bloemfontein, South Africa.
   Rudolph, Elizabeth M., Univ Free State, Afromontane Res Unit, Dept Geog, Bloemfontein, South Africa.
   Hedding, David W., Univ South Africa, Dept Geog, Johannesburg, South Africa.
   De Bruyn, P. J. Nico, Univ Pretoria, Mammal Res Inst, Dept Zool \& Entomol, Pretoria, South Africa.
   Nel, Werner, Univ Ft Hare, Dept Geog \& Environm Sci, Alice, South Africa.},
DOI = {10.17159/sajs.2022/12302},
Article-Number = {12302},
ISSN = {0038-2353},
EISSN = {1996-7489},
Keywords = {Prince Edward Island; Marion Island; geospatial database; open access;
   data sharing},
Keywords-Plus = {CLIMATE-CHANGE},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {rudolphem@ufs.ac.za},
Affiliations = {University of the Free State; University of South Africa; University of
   Pretoria; University of Fort Hare},
ResearcherID-Numbers = {Hedding, David William/F-3044-2011
   de Bruyn, P. J. Nico/E-4176-2010
   },
ORCID-Numbers = {Hedding, David William/0000-0002-9748-4499
   de Bruyn, P. J. Nico/0000-0002-9114-9569
   Nel, Werner/0000-0002-3769-4937},
Funding-Acknowledgement = {South African National Research Foundation {[}SANAP-NRF: 129235, 129228]},
Funding-Text = {South African National Research Foundation (SANAP-NRF: 129235; 129228)},
Number-of-Cited-References = {60},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {S. Afr. J. Sci.},
Doc-Delivery-Number = {6I4HR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000886088500022},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000485885100001,
Author = {Mendez, Kevin M. and Pritchard, Leighton and Reinke, Stacey N. and
   Broadhurst, David I.},
Title = {Toward collaborative open data science in metabolomics using Jupyter
   Notebooks and cloud computing},
Journal = {METABOLOMICS},
Year = {2019},
Volume = {15},
Number = {10},
Month = {OCT},
Abstract = {Background A lack of transparency and reporting standards in the
   scientific community has led to increasing and widespread concerns
   relating to reproduction and integrity of results. As an omics science,
   which generates vast amounts of data and relies heavily on data science
   for deriving biological meaning, metabolomics is highly vulnerable to
   irreproducibility. The metabolomics community has made substantial
   efforts to align with FAIR data standards by promoting open data
   formats, data repositories, online spectral libraries, and metabolite
   databases. Open data analysis platforms also exist; however, they tend
   to be inflexible and rely on the user to adequately report their methods
   and results. To enable FAIR data science in metabolomics, methods and
   results need to be transparently disseminated in a manner that is rapid,
   reusable, and fully integrated with the published work. To ensure broad
   use within the community such a framework also needs to be inclusive and
   intuitive for both computational novices and experts alike. Aim of
   Review To encourage metabolomics researchers from all backgrounds to
   take control of their own data science, mould it to their personal
   requirements, and enthusiastically share resources through open science.
   Key Scientific Concepts of Review This tutorial introduces the concept
   of interactive web-based computational laboratory notebooks. The reader
   is guided through a set of experiential tutorials specifically targeted
   at metabolomics researchers, based around the Jupyter Notebook web
   application, GitHub data repository, and Binder cloud computing
   platform.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Review},
Language = {English},
Affiliation = {Reinke, SN; Broadhurst, DI (Corresponding Author), Edith Cowan Univ, Sch Sci, Ctr Metabol \& Computat Biol, Joondalup 6027, Australia.
   Mendez, Kevin M.; Reinke, Stacey N.; Broadhurst, David I., Edith Cowan Univ, Sch Sci, Ctr Metabol \& Computat Biol, Joondalup 6027, Australia.
   Pritchard, Leighton, Univ Strathclyde, Strathclyde Inst Pharm \& Biomed Sci, Cathedral St, Glasgow G1 1XQ, Lanark, Scotland.},
DOI = {10.1007/s11306-019-1588-0},
Article-Number = {125},
ISSN = {1573-3882},
EISSN = {1573-3890},
Keywords = {Open access; Reproducibility; Data science; Statistics; Cloud computing;
   Jupyter},
Keywords-Plus = {REPOSITORY; VISUALIZATION; STANDARDS},
Research-Areas = {Endocrinology \& Metabolism},
Web-of-Science-Categories  = {Endocrinology \& Metabolism},
Author-Email = {stacey.n.reinke@ecu.edu.au
   d.broadhurst@ecu.edu.au},
Affiliations = {Edith Cowan University; University of Strathclyde},
ResearcherID-Numbers = {Pritchard, Leighton/A-7331-2008
   },
ORCID-Numbers = {Pritchard, Leighton/0000-0002-8392-2822
   Broadhurst, David/0000-0003-0775-9581
   Reinke, Stacey/0000-0002-0758-0330
   Mendez, Kevin/0000-0002-8832-2607},
Funding-Acknowledgement = {Australian Research Council {[}LE170100021]; Australian Research Council
   {[}LE170100021] Funding Source: Australian Research Council},
Funding-Text = {This work was partly funded through an Australian Research Council
   funded LIEF Grant No. (LE170100021).},
Number-of-Cited-References = {51},
Times-Cited = {44},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {20},
Journal-ISO = {Metabolomics},
Doc-Delivery-Number = {IX7SL},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000485885100001},
OA = {Green Published, hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:001093820000001,
Author = {Mosha, Neema Florence and Ngulube, Patrick},
Title = {The utilisation of open research data repositories for storing and
   sharing research data in higher learning institutions in Tanzania},
Journal = {LIBRARY MANAGEMENT},
Year = {2023},
Volume = {44},
Number = {8/9},
Pages = {566-580},
Month = {NOV 14},
Abstract = {PurposeThe study aims to investigate the utilisation of open research
   data repositories (RDRs) for storing and sharing research data in higher
   learning institutions (HLIs) in Tanzania.Design/methodology/approachA
   survey research design was employed to collect data from postgraduate
   students at the Nelson Mandela African Institution of Science and
   Technology (NM-AIST) in Arusha, Tanzania. The data were collected and
   analysed quantitatively and qualitatively. A census sampling technique
   was employed to select the sample size for this study. The quantitative
   data were analysed using the Statistical Package for the Social Sciences
   (SPSS), whilst the qualitative data were analysed
   thematically.FindingsLess than half of the respondents were aware of and
   were using open RDRs, including Zenodo, DataVerse, Dryad, OMERO, GitHub
   and Mendeley data repositories. More than half of the respondents were
   not willing to share research data and cited a lack of ownership after
   storing their research data in most of the open RDRs and data security.
   HILs need to conduct training on using trusted repositories and motivate
   postgraduate students to utilise open repositories (ORs). The challenges
   for underutilisation of open RDRs were a lack of policies governing the
   storage and sharing of research data and grant
   constraints.Originality/valueResearch data storage and sharing are of
   great interest to researchers in HILs to inform them to implement open
   RDRs to support these researchers. Open RDRs increase visibility within
   HILs and reduce research data loss, and research works will be cited and
   used publicly. This paper identifies the potential for additional
   studies focussed on this area.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {Floor 5, Northspring 21-23 Wellington Street, Leeds, W YORKSHIRE,
   ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Mosha, NF (Corresponding Author), Univ South Africa, Coll Grad Studies, Muckleneuk Campus, Pretoria, South Africa.
   Mosha, Neema Florence, Univ South Africa, Coll Grad Studies, Muckleneuk Campus, Pretoria, South Africa.
   Ngulube, Patrick, Univ South Africa, Dept Interdisciplinary Res \& Postgrad Studies, Pretoria, South Africa.},
DOI = {10.1108/LM-05-2023-0042},
EarlyAccessDate = {OCT 2023},
ISSN = {0143-5124},
EISSN = {1758-7921},
Keywords = {Tanzania; Research data; Higher learning institutions; Research data
   sharing; Open research data repositories; Research data storage},
Keywords-Plus = {OPEN SCIENCE; PRINCIPLES},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {moshanf@unisa.ac.za},
Affiliations = {University of South Africa; University of South Africa},
ORCID-Numbers = {Ngulube, Patrick/0000-0002-7676-3931},
Funding-Acknowledgement = {The authors acknowledge the help and support provided by many people for
   this work. The work described took place alongside the corresponding
   authorapos;s postdoctoral research fellow at the University of South
   Africa (UNISA), Pretoria, South Africa, in c; Nelson Mandela Africa
   Institution of Science and Technology (NM-AIST) in Arusha, Tanzania},
Funding-Text = {The authors acknowledge the help and support provided by many people for
   this work. The work described took place alongside the corresponding
   author \& apos;s postdoctoral research fellow at the University of South
   Africa (UNISA), Pretoria, South Africa, in collaboration with mentor
   Professor Patrick Ngulube. The corresponding author also thanks the
   respondents, postgraduate students from 2021 to 2022 at the Nelson
   Mandela Africa Institution of Science and Technology (NM-AIST) in
   Arusha, Tanzania.},
Number-of-Cited-References = {54},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Libr. Manage.},
Doc-Delivery-Number = {X1UZ9},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001093820000001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000540078900001,
Author = {Walters, William H.},
Title = {Data journals: incentivizing data access and documentation within the
   scholarly communication system},
Journal = {INSIGHTS-THE UKSG JOURNAL},
Year = {2020},
Volume = {33},
Month = {JUN 10},
Abstract = {Data journals provide strong incentives for data creators to verify,
   document and disseminate their data. They also bring data access and
   documentation into the mainstream of scholarly communication, rewarding
   data creators through existing mechanisms of peer-reviewed publication
   and citation tracking. These same advantages are not generally
   associated with data repositories, or with conventional journals'
   data-sharing mandates. This article describes the unique advantages of
   data journals. It also examines the data journal landscape, presenting
   the characteristics of 13 data journals in the fields of biology,
   environmental science, chemistry, medicine and health sciences. These
   journals vary considerably in size, scope, publisher characteristics,
   length of data reports, data hosting policies, time from submission to
   first decision, article processing charges, bibliographic index coverage
   and citation impact. They are similar, however, in their peer review
   criteria, their open access license terms and the characteristics of
   their editorial boards.},
Publisher = {UBIQUITY PRESS LTD},
Address = {2N, 6 OSBORNE ST, LONDON, E1 6TD, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Walters, WH (Corresponding Author), Manhattan Coll, Mary Alice \& Tom OMalley Lib, New York, NY 10471 USA.
   Walters, William H., Manhattan Coll, Mary Alice \& Tom OMalley Lib, New York, NY 10471 USA.},
DOI = {10.1629/uksg.510},
Article-Number = {18},
ISSN = {2048-7754},
Keywords = {data journals; data repositories; incentives; open access; open data},
Keywords-Plus = {METRICS},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {william.walters@manhattan.edu},
Affiliations = {Manhattan College},
ResearcherID-Numbers = {Walters, William H./GRS-6674-2022
   },
ORCID-Numbers = {Walters, William/0000-0001-9490-4032},
Number-of-Cited-References = {47},
Times-Cited = {15},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {30},
Journal-ISO = {Insights},
Doc-Delivery-Number = {LX8LX},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000540078900001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000784323700002,
Author = {Zhou, Bingjie and Liang, Shiwei and Monahan, Kyle M. and El-Abbadi,
   Naglaa and Cruz, Melissa S. and Chen, Yutong and DeVane, Annie and
   Reedy, Julia and Zhang, Jianyi and Semenova, Iaroslava and Montoliu,
   Ivan and Mozaffarian, Dariush and Wang, Dantong and Naumova, Elena N.},
Title = {An Open-Access Data Platform: Global Nutrition and Health Atlas (GNHA)},
Journal = {CURRENT DEVELOPMENTS IN NUTRITION},
Year = {2022},
Volume = {6},
Number = {4},
Month = {APR 13},
Abstract = {The rapid development of nutrition science is embracing digital
   transformation to generate large amounts of data. Precision nutrition
   and ``Big Data{''} place increasing demand for data repositories and
   visualization, which enhances the digital transformation. We defined the
   need for an integrated nutrition data platform as a web-based platform
   that can collect, store, track, analyze, monitor, and visually display
   key metrics in nutrition and health while allowing users to interact
   with visuals and download data provided in the platform. Interactive
   dashboards create new opportunities for scholars and practitioners to
   generate and test hypotheses. We present the development and
   implementation of the Global Nutrition and Health Atlas (GNHA;
   https://sites.tufts.edu/gnha/), an open-access online platform covering
   nutrition and health data with 26 themes and 500+ indicators from 190+
   countries up to 30 y. We view GNHA as an interactive tool aiming to
   share information and perspectives and foster collaborations and
   innovations.},
Publisher = {OXFORD UNIV PRESS INC},
Address = {JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
Type = {Article},
Language = {English},
Affiliation = {Naumova, EN (Corresponding Author), Tufts Univ, Friedman Sch Nutr Sci \& Policy, Boston, MA 02111 USA.
   Zhou, Bingjie; Liang, Shiwei; El-Abbadi, Naglaa; Cruz, Melissa S.; Chen, Yutong; DeVane, Annie; Reedy, Julia; Zhang, Jianyi; Mozaffarian, Dariush; Naumova, Elena N., Tufts Univ, Friedman Sch Nutr Sci \& Policy, Boston, MA 02111 USA.
   Monahan, Kyle M., Tufts Univ, Tufts Technol Serv, Data Lab, Medford, MA 02155 USA.
   Semenova, Iaroslava; Montoliu, Ivan; Wang, Dantong, Nestle Res, Nestle Inst Hlth Sci, Lausanne, Switzerland.},
Article-Number = {nzac031},
ISSN = {2475-2991},
Keywords = {dashboard; data repository; food system; nutrition; visualization},
Research-Areas = {Nutrition \& Dietetics},
Web-of-Science-Categories  = {Nutrition \& Dietetics},
Author-Email = {elena.naumova@tufts.edu},
Affiliations = {Tufts University; Tufts University; Nestle SA},
ResearcherID-Numbers = {Naumova, Elena/AAP-3395-2020
   },
ORCID-Numbers = {Naumova, Elena/0000-0002-9562-4734
   Liang, Shiwei/0000-0001-7845-3534
   Wang, Dantong/0000-0003-2379-8222
   Zhang, Jianyi/0000-0002-1501-4822
   Zhou, Bingjie/0000-0002-9776-0414},
Funding-Acknowledgement = {Societe des Produits Nestle SA},
Funding-Text = {Supported by Societe des Produits Nestle SA.},
Number-of-Cited-References = {14},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Curr. Dev. Nutr.},
Doc-Delivery-Number = {0P6FY},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000784323700002},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000485809100005,
Author = {AlRyalat, Saif Aldeen and Abu Nassar, Anas and Tamimi, Faris and
   Al-Fraihat, Esraa and Assaf, Lama and Ghareeb, Razan and Masoudi,
   Mahmoud and Al-Essa, Mohammad},
Title = {The Impact of Open-Access Status on Journal Indices: Respiratory and
   Pulmonology Journals},
Journal = {CURRENT RESPIRATORY MEDICINE REVIEWS},
Year = {2019},
Volume = {15},
Number = {1},
Pages = {26-31},
Abstract = {Background: Open access (OA) publishing is rapidly emerging in almost
   all disciplines, with variable intensity and effect on the discipline
   itself. The move toward OA is also observed in the field of respiratory
   and pulmonology, where both OA data repositories and OA journals are
   rapidly emerging.
   Objective: we aim to study the open-access status of respiratory and
   pulmonology journals and the impact of the open-access status on journal
   indices.
   Methods: We collected journal's data from Scopus Source List on 1st of
   November 2018. We filtered the list for respiratory and pulmonology
   journals. Open Access Journals covered by Scopus are recognized as Open
   Access if the journal is listed in the Directory of Open Access Journals
   (DOAJ) and/or the Directory of Open Access Scholarly Resources (ROAD).
   For each journal, we used several metrics to measure its strength, and
   then we compared these metrics between OA and non-OA journals.
   Results: There were 125 respiratory and pulmonology journals, a number
   that has increased by 12.6\% since 2011. Moreover, the percentage of OA
   journals has increased from 21.6\% to 26.4\% during the same period.
   Non-OA journals have significantly higher scholarly output (p=0.033),
   but OA journals have significantly higher percentage of citation
   (p=0.05).
   Conclusion: Publishing in OA journals will yield a higher citation
   percentage compared to non-OA journals. Although this should not be the
   only reason to publish in an OA journal, it is still an important factor
   to decide where to publish.},
Publisher = {BENTHAM SCIENCE PUBL LTD},
Address = {EXECUTIVE STE Y-2, PO BOX 7917, SAIF ZONE, 1200 BR SHARJAH, U ARAB
   EMIRATES},
Type = {Article},
Language = {English},
Affiliation = {AlRyalat, SA (Corresponding Author), Univ Jordan, Univ Jordan Hosp, Dept Ophthalmol, Amman 11942, Jordan.
   AlRyalat, Saif Aldeen, Univ Jordan, Univ Jordan Hosp, Dept Ophthalmol, Amman 11942, Jordan.
   Abu Nassar, Anas; Tamimi, Faris; Al-Essa, Mohammad, King Hussein Canc Ctr, Amman 11942, Jordan.
   Al-Fraihat, Esraa, Univ Jordan, Dept Pathol \& Microbiol \& Forens Med, Amman 11942, Jordan.
   Assaf, Lama, Univ Jordan, Univ Jordan Hosp, Dept Anesthesia, Amman 11942, Jordan.
   Ghareeb, Razan; Masoudi, Mahmoud, Univ Jordan, Dept Internal Med, Amman 11942, Jordan.},
DOI = {10.2174/1573398X15666190214154531},
ISSN = {1573-398X},
EISSN = {1875-6387},
Keywords = {Bibliometry; journals; open access; pulmonology; respiratory; impact},
Research-Areas = {Respiratory System},
Web-of-Science-Categories  = {Respiratory System},
Author-Email = {saifryalat@yahoo.com},
Affiliations = {University of Jordan; King Hussein Cancer Center; University of Jordan;
   University of Jordan; University of Jordan},
ResearcherID-Numbers = {Tamimi, Faris/HHY-7324-2022
   AlRyalat, Saif Aldeen/J-7528-2016},
ORCID-Numbers = {Tamimi, Faris/0000-0002-9337-6618
   AlRyalat, Saif Aldeen/0000-0001-5588-9458},
Number-of-Cited-References = {16},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Curr. Respir. Med. Rev.},
Doc-Delivery-Number = {IX6QL},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000485809100005},
DA = {2024-01-15},
}

@article{ WOS:000651707700001,
Author = {Das, Samir and Abou-Haidar, Rida and Rabalais, Henri and Sun, Sonia
   Denise Lai Wing and Rosli, Zaliqa and Chatpar, Krishna and Boivin,
   Marie-Noelle and Tabatabaei, Mahdieh and Rogers, Christine and Legault,
   Melanie and Lo, Derek and Degroot, Clotilde and Dagher, Alain and Dyke,
   Stephanie O. M. and Durcan, Thomas M. and Seyller, Annabel and Doyon,
   Julien and Poupon, Viviane and Fon, Edward A. and Genge, Angela and
   Rouleau, Guy A. and Karamchandani, Jason and Evans, Alan C.},
Title = {The C-BIG Repository: an Institution-Level Open Science Platform},
Journal = {NEUROINFORMATICS},
Year = {2022},
Volume = {20},
Number = {1},
Pages = {139-153},
Month = {JAN},
Abstract = {In January 2016, the Montreal Neurological Institute-Hospital (The
   Neuro) declared itself an Open Science organization. This vision extends
   beyond efforts by individual scientists seeking to release individual
   datasets, software tools, or building platforms that provide for the
   free dissemination of such information. It involves multiple
   stakeholders and an infrastructure that considers governance, ethics,
   computational resourcing, physical design, workflows, training,
   education, and intra-institutional reporting structures. The C-BIG
   repository was built in response as The Neuro's institutional
   biospecimen and clinical data repository, and collects biospecimens as
   well as clinical, imaging, and genetic data from patients with
   neurological disease and healthy controls. It is aimed at helping
   scientific investigators, in both academia and industry, advance our
   understanding of neurological diseases and accelerate the development of
   treatments. As many neurological diseases are quite rare, they present
   several challenges to researchers due to their small patient
   populations. Overcoming these challenges required the aggregation of
   datasets from various projects and locations. The C-BIG repository
   achieves this goal and stands as a scalable working model for
   institutions to collect, track, curate, archive, and disseminate
   multimodal data from patients. In November 2020, a Registered Access
   layer was made available to the wider research community at
   https://cbigr-open.loris.ca, and in May 2021 fully open data will be
   released to complement the Registered Access data. This article outlines
   many of the aspects of The Neuro's transition to Open Science by
   describing the data to be released, C-BIG's full capabilities, and the
   design aspects that were implemented for effective data sharing.},
Publisher = {HUMANA PRESS INC},
Address = {999 RIVERVIEW DRIVE SUITE 208, TOTOWA, NJ 07512 USA},
Type = {Article},
Language = {English},
Affiliation = {Das, S (Corresponding Author), McGill Univ, McGill Ctr Integrat Neurosci, Montreal, PQ, Canada.
   Das, S (Corresponding Author), Montreal Neurol Inst Hosp, Montreal, PQ, Canada.
   Das, S (Corresponding Author), Montreal Neurol Inst Hosp, McConnell Brain Imaging Ctr, Montreal, PQ, Canada.
   Das, Samir; Abou-Haidar, Rida; Rabalais, Henri; Rosli, Zaliqa; Chatpar, Krishna; Rogers, Christine; Legault, Melanie; Lo, Derek; Dyke, Stephanie O. M.; Evans, Alan C., McGill Univ, McGill Ctr Integrat Neurosci, Montreal, PQ, Canada.
   Das, Samir; Abou-Haidar, Rida; Rabalais, Henri; Sun, Sonia Denise Lai Wing; Rosli, Zaliqa; Chatpar, Krishna; Boivin, Marie-Noelle; Tabatabaei, Mahdieh; Rogers, Christine; Legault, Melanie; Lo, Derek; Degroot, Clotilde; Dagher, Alain; Dyke, Stephanie O. M.; Seyller, Annabel; Doyon, Julien; Poupon, Viviane; Fon, Edward A.; Genge, Angela; Rouleau, Guy A.; Karamchandani, Jason; Evans, Alan C., Montreal Neurol Inst Hosp, Montreal, PQ, Canada.
   Das, Samir; Dagher, Alain; Doyon, Julien; Evans, Alan C., Montreal Neurol Inst Hosp, McConnell Brain Imaging Ctr, Montreal, PQ, Canada.
   Sun, Sonia Denise Lai Wing; Durcan, Thomas M.; Genge, Angela; Karamchandani, Jason, McGill Univ, Clin Res Unit, Montreal, PQ, Canada.
   Dyke, Stephanie O. M.; Fon, Edward A., McGill Univ, Dept Neurol \& Neurosurg, Montreal, PQ, Canada.
   Durcan, Thomas M., Montreal Neurol Inst Hosp, Early Drug Discovery Unit EDDU, Montreal, PQ, Canada.},
DOI = {10.1007/s12021-021-09516-9},
EarlyAccessDate = {MAY 2021},
ISSN = {1539-2791},
EISSN = {1559-0089},
Keywords = {Open Science; Database; Genetic; Registered access; Biobank;
   Interoperability},
Keywords-Plus = {ACCESS},
Research-Areas = {Computer Science; Neurosciences \& Neurology},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Neurosciences},
Author-Email = {samir.das@mcgill.ca},
Affiliations = {McGill University; McGill University; McGill University; McGill
   University; McGill University; McGill University},
ORCID-Numbers = {Das, Samir/0000-0003-2018-8760
   Boivin, Marie-Noelle/0009-0000-6073-9286
   Karamchandani, Jason/0000-0002-3906-5616
   Seyller, Annabel/0000-0002-2168-3125},
Funding-Acknowledgement = {CIHR Foundation {[}FDN -154301]; Canada Research Chair (Tier 1) in
   Parkinson's disease; McGill's Healthy Brains for Healthy Lives
   initiative; Brain Canada {[}4523]},
Funding-Text = {E.A.F is supported by a CIHR Foundation grant (FDN -154301) and by a
   Canada Research Chair (Tier 1) in Parkinson's disease. Support also
   provided for specific aspects from McGill's Healthy Brains for Healthy
   Lives initiative. Support from Brain Canada (ID \#4523). The Neuro
   provided key institutional support. Philanthropic support was given from
   the Larry and Judy Tanenbaum family.},
Number-of-Cited-References = {38},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Neuroinformatics},
Doc-Delivery-Number = {5D0ZP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000651707700001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:001013720000001,
Author = {Hamzah, Nurfaten and Malim, Nurul Hashimah Ahamed Hassain and Abdullah,
   Jafri Malin and Sumari, Putra and Mokhtar, Ariffin Marzuki and Rosli,
   Siti Nur Syamila and Ibrahim, Sharifah Aida Shekh and Idris, Zamzuri},
Title = {Big Brain Data Initiatives in Universiti Sains Malaysia: Data
   Stewardship to Data Repository and Data Sharing},
Journal = {NEUROINFORMATICS},
Year = {2023},
Volume = {21},
Number = {3},
Pages = {589-600},
Month = {JUL},
Abstract = {The sharing of open-access neuroimaging data has increased significantly
   during the last few years. Sharing neuroimaging data is crucial to
   accelerating scientific advancement, particularly in the field of
   neuroscience. A number of big initiatives that will increase the amount
   of available neuroimaging data are currently in development. The Big
   Brain Data Initiative project was started by Universiti Sains Malaysia
   as the first neuroimaging data repository platform in Malaysia for the
   purpose of data sharing. In order to ensure that the neuroimaging data
   in this project is accessible, usable, and secure, as well as to offer
   users high-quality data that can be consistently accessed, we first came
   up with good data stewardship practices. Then, we developed MyneuroDB,
   an online repository database system for data sharing purposes. Here, we
   describe the Big Brain Data Initiative and MyneuroDB, a data repository
   that provides the ability to openly share neuroimaging data, currently
   including magnetic resonance imaging (MRI), electroencephalography
   (EEG), and magnetoencephalography (MEG), following the FAIR principles
   for data sharing.},
Publisher = {HUMANA PRESS INC},
Address = {999 RIVERVIEW DRIVE SUITE 208, TOTOWA, NJ 07512 USA},
Type = {Article},
Language = {English},
Affiliation = {Malim, NHAH (Corresponding Author), Univ Sains Malaysia, Sch Comp Sci, Gelugor 11800, Pulau Pinang, Malaysia.
   Hamzah, Nurfaten; Abdullah, Jafri Malin; Rosli, Siti Nur Syamila; Idris, Zamzuri, Univ Sains Malaysia, Sch Med Sci, Dept Neurosci, Hlth Campus, Kubang Kerian 16150, Kelantan, Malaysia.
   Malim, Nurul Hashimah Ahamed Hassain; Sumari, Putra; Ibrahim, Sharifah Aida Shekh, Univ Sains Malaysia, Sch Comp Sci, Gelugor 11800, Pulau Pinang, Malaysia.
   Hamzah, Nurfaten; Abdullah, Jafri Malin; Idris, Zamzuri, Univ Sains Malaysia, Sch Med Sci, Brain \& Behav Cluster, Hlth Campus, Kubang Kerian 16150, Kelantan, Malaysia.
   Abdullah, Jafri Malin, Univ Sains Malaysia, Hosp Univ Sains Malaysia, Dept Neurosci, Hlth Campus, Kubang Kerian 16150, Kelantan, Malaysia.
   Abdullah, Jafri Malin, Univ Sains Malaysia, Hosp Univ Sains Malaysia, Brain Behav Cluster, Hlth Campus, Kubang Kerian 16150, Kelantan, Malaysia.
   Mokhtar, Ariffin Marzuki, Univ Sains Malaysia, Hosp Univ Sains Malaysia, Hosp Management Syst Unit, Hlth Campus, Kubang Kerian 16150, Kelantan, Malaysia.},
DOI = {10.1007/s12021-023-09637-3},
EarlyAccessDate = {JUN 2023},
ISSN = {1539-2791},
EISSN = {1559-0089},
Keywords = {Neuroimaging technique; Neuroimaging data; Data stewardship; Data
   repository; Data sharing},
Keywords-Plus = {NEUROIMAGING DATA},
Research-Areas = {Computer Science; Neurosciences \& Neurology},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Neurosciences},
Author-Email = {nurfaten@usm.my
   nurulhashimah@usm.my
   brainsciences@gmail.com
   putras@usm.my
   ariffinm@usm.my
   syamilarosli@usm.my
   aidashaza@gmail.com
   zamzuri@usm.my},
Affiliations = {Universiti Sains Malaysia; Universiti Sains Malaysia; Universiti Sains
   Malaysia; Universiti Sains Malaysia; Universiti Sains Malaysia;
   Universiti Sains Malaysia},
ResearcherID-Numbers = {Hamzah, Nurfaten/B-7359-2018
   Sumari, Putra/I-1070-2016
   Abdullah, Jafri Malin/C-2828-2011
   },
ORCID-Numbers = {Hamzah, Nurfaten/0000-0001-6272-1143
   Sumari, Putra/0000-0002-2644-6428
   Ahamed Hassain Malim, Nurul Hashimah/0000-0002-5652-9152
   Abdullah, Jafri Malin/0000-0002-0258-7410
   Idris, Zamzuri/0000-0002-9470-0571},
Number-of-Cited-References = {37},
Times-Cited = {0},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Neuroinformatics},
Doc-Delivery-Number = {O1MS0},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001013720000001},
DA = {2024-01-15},
}

@article{ WOS:000691563800007,
Author = {Bolkovac, Jelena and Krajna, Tamara and Petrak, Jelka},
Title = {Research Data of Croatian Authors on the Web of Science Platform},
Journal = {KEMIJA U INDUSTRIJI-JOURNAL OF CHEMISTS AND CHEMICAL ENGINEERS},
Year = {2021},
Volume = {70},
Number = {9-10},
Pages = {543-549},
Abstract = {Open access to research data is an important part of the concept of open
   science. The aim of this article was to identify Croatian
   authors/institutions that have recognized the importance of sharing
   research data, and that have given them access via one of the data
   repositories covered by Data Citation Index. A total of 265 documents
   were found in the database. Data papers by Croatian authors available on
   the Web of Science Core Collection platform were also analysed.
   Twenty-nine of them were found, mostly of multidisciplinary orientation.
   The authors of the largest number of data documents are affiliated to
   the University of Zagreb. Croatian researchers are archiving data in
   international repositories, because the infrastructure for their
   archiving at the national level has only recently been developed, and is
   just beginning to be used.},
Publisher = {HRVATSKO DRUSTVO KEMJIJSKIH INZENJERA I TEHNOLOGA},
Address = {BERISLAVICEVA 6-1 P O BOX 123, 41001 ZAGREB, CROATIA},
Type = {Article},
Language = {Croatian},
Affiliation = {Krajna, T (Corresponding Author), Sveuciliste Zagrebu, Fak Strojarstva \& Brodogradnje, Ivana Lucica 5, Zagreb 10000, Croatia.
   Bolkovac, Jelena; Krajna, Tamara, Sveuciliste Zagrebu, Fak Strojarstva \& Brodogradnje, Ivana Lucica 5, Zagreb 10000, Croatia.
   Petrak, Jelka, Sveuciliste Zagrebu, Med Fak, Salata 3, Zagreb 10000, Croatia.},
DOI = {10.15255/KUI.2021.034},
ISSN = {0022-9830},
EISSN = {1334-9090},
Keywords = {Open science; research data; data papers; data repositories},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary},
Author-Email = {tkrajna@fsb.hr},
Affiliations = {University of Zagreb; University of Zagreb Faculty of Mechanical
   Engineering \& Naval Architecture; University of Zagreb},
ResearcherID-Numbers = {Krajna, Tamara/A-1841-2013
   Petrak, Jelka/B-5392-2011
   Bolkovac, Jelena/W-9865-2018},
ORCID-Numbers = {Krajna, Tamara/0000-0002-5132-8765
   Petrak, Jelka/0000-0003-1481-2598
   },
Number-of-Cited-References = {31},
Times-Cited = {0},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Kem. Ind.},
Doc-Delivery-Number = {UJ8XZ},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000691563800007},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000570190900006,
Author = {Kras, Ashley and Celi, Leo A. and Miller, John B.},
Title = {Accelerating ophthalmic artificial intelligence research: the role of an
   open access data repository},
Journal = {CURRENT OPINION IN OPHTHALMOLOGY},
Year = {2020},
Volume = {31},
Number = {5},
Pages = {337-350},
Month = {SEP},
Abstract = {Purpose of review Artificial intelligence has already provided multiple
   clinically relevant applications in ophthalmology. Yet, the explosion of
   nonstandardized reporting of high-performing algorithms are rendered
   useless without robust and streamlined implementation guidelines. The
   development of protocols and checklists will accelerate the translation
   of research publications to impact on patient care. Recent findings
   Beyond technological scepticism, we lack uniformity in analysing
   algorithmic performance generalizability, and benchmarking impacts
   across clinical settings. No regulatory guardrails have been set to
   minimize bias or optimize interpretability; no consensus clinical
   acceptability thresholds or systematized postdeployment monitoring has
   been set. Moreover, stakeholders with misaligned incentives deepen the
   landscape complexity especially when it comes to the requisite data
   integration and harmonization to advance the field. Therefore, despite
   increasing algorithmic accuracy and commoditization, the infamous
   `implementation gap' persists. Open clinical data repositories have been
   shown to rapidly accelerate research, minimize redundancies and
   disseminate the expertise and knowledge required to overcome existing
   barriers. Drawing upon the longstanding success of existing governance
   frameworks and robust data use and sharing agreements, the ophthalmic
   community has tremendous opportunity in ushering artificial intelligence
   into medicine. By collaboratively building a powerful resource of open,
   anonymized multimodal ophthalmic data, the next generation of clinicians
   can advance data-driven eye care in unprecedented ways. This piece
   demonstrates that with readily accessible data, immense progress can be
   achieved clinically and methodologically to realize artificial
   intelligence's impact on clinical care. Exponentially progressive
   network effects can be seen by consolidating, curating and distributing
   data amongst both clinicians and data scientists.},
Publisher = {LIPPINCOTT WILLIAMS \& WILKINS},
Address = {TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA, PA 19103 USA},
Type = {Review},
Language = {English},
Affiliation = {Miller, JB (Corresponding Author), Harvard Med Sch, Massachusetts Eye \& Ear, Retinal Imaging, 243 Charles St, Boston, MA 02114 USA.
   Miller, JB (Corresponding Author), Harvard Med Sch, Ophthalmol, 243 Charles St, Boston, MA 02114 USA.
   Kras, Ashley; Miller, John B., Harvard Med Sch, Dept Ophthalmol, Massachusetts Eye \& Ear, Harvard Retinal Imaging Lab, Boston, MA 02115 USA.
   Celi, Leo A., Harvard Med Sch, MIT, Harvard MIT Div Hlth Sci \& Technol, Cambridge, MA USA.
   Celi, Leo A., Harvard Med Sch, Beth Israel Deaconess Med Ctr, Dept Med, Boston, MA 02115 USA.
   Miller, John B., Harvard Med Sch, Dept Ophthalmol, Massachusetts Eye \& Ear, Retina Serv, Boston, MA 02115 USA.},
DOI = {10.1097/ICU.0000000000000678},
ISSN = {1040-8738},
EISSN = {1531-7021},
Keywords = {artificial intelligence; open-source; translational big data},
Keywords-Plus = {HEALTH-CARE PROFESSIONALS; DEEP LEARNING ALGORITHM;
   DIABETIC-RETINOPATHY; RISK-FACTORS; PREDICTION; CLASSIFICATION;
   SEGMENTATION; INFORMATION; PHOTOGRAPHY; PERFORMANCE},
Research-Areas = {Ophthalmology},
Web-of-Science-Categories  = {Ophthalmology},
Author-Email = {john\_miller@meei.harvard.edu},
Affiliations = {Harvard University; Harvard Medical School; Massachusetts Eye \& Ear
   Infirmary; Harvard University; Massachusetts Institute of Technology
   (MIT); Harvard University; Beth Israel Deaconess Medical Center; Harvard
   Medical School; Harvard University; Harvard Medical School;
   Massachusetts Eye \& Ear Infirmary},
ResearcherID-Numbers = {Miller, John J/GZG-5663-2022},
Funding-Acknowledgement = {National Institute of Health through NIBIB {[}R01 EB017205]},
Funding-Text = {L.A.C. is funded by the National Institute of Health through NIBIB R01
   EB017205.},
Number-of-Cited-References = {94},
Times-Cited = {16},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Curr. Opin. Ophthalmol.},
Doc-Delivery-Number = {NP5BI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000570190900006},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000430568506077,
Author = {Tkachenko, Valery and Zakharov, Richard and Presniakov, Igor and
   Kalmykov, Stepan},
Title = {Open Science Data Repository - the platform for materials research},
Journal = {ABSTRACTS OF PAPERS OF THE AMERICAN CHEMICAL SOCIETY},
Year = {2017},
Volume = {253},
Meeting = {170},
Month = {APR 2},
Note = {253rd National Meeting of the American-Chemical-Society (ACS) on
   Advanced Materials, Technologies, Systems, and Processes, San Francisco,
   CA, APR 02-06, 2017},
Organization = {Amer Chem Soc},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Meeting Abstract},
Language = {English},
Affiliation = {Tkachenko, Valery; Zakharov, Richard, SCI DATA SOFTWARE LLC, Rockville, MD USA.
   Presniakov, Igor; Kalmykov, Stepan, Moscow MV Lomonosov State Univ, Dept Chem, Moscow, Russia.},
ISSN = {0065-7727},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary},
Author-Email = {2388838@acs.org},
Affiliations = {Lomonosov Moscow State University},
ResearcherID-Numbers = {Kalmykov, Stepan N./Q-9757-2017},
ORCID-Numbers = {Kalmykov, Stepan N./0000-0002-2396-4561},
Number-of-Cited-References = {0},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Abstr. Pap. Am. Chem. Soc.},
Doc-Delivery-Number = {GD5TC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Conference Proceedings Citation Index - Science (CPCI-S)},
Unique-ID = {WOS:000430568506077},
DA = {2024-01-15},
}

@article{ WOS:001127416700002,
Author = {Silva, Vivian dos Santos and da Silva, Jesiel Viana and Dias, Thiago
   Magela Rodrigues and Gabriel Junior, Rene Faustino and Segundo,
   Washington Luis Ribeiro de Carvalho},
Title = {BrCris: tools for treatment, analysis, and dissemination of scientific
   information in support of Open Science in Brazil},
Journal = {RDBCI-REVISTA DIGITAL DE BIBLIOTECONOMIA E CIENCIA DA INFORMACAO},
Year = {2023},
Volume = {21},
Abstract = {Introduction: CRIS systems constitute comprehensive information systems
   over the entire ecosystem of the scientific process. BrCris aims to
   integrate and organize information regarding research activities,
   projects, publications, researchers, institutions, financing and other
   relevant data in the Brazilian scientific context. Objective: This study
   aims to discuss data processing on the BrCris Platform and analyze the
   computational tools used for this purpose, exploring three main
   approaches: data integration and consistency, visualization and
   validation, in addition to data certification. Methodology: The study is
   descriptive, presenting in detail the BrCris data processing steps,
   discussing the challenges encountered in handling large volumes of
   information. Furthermore, it describes the computational tools used to
   process scientific and technological information. Results: The study
   reveals the procedures for data processing and the computational tools
   developed for information systems, as well as the integration and
   analysis of the data obtained. The results of the processing and
   modeling of information based on VIVO, with data and graphic panels, and
   the opportunities for reusing the generated data are presented. The
   integration of data into a self-declared repository (Lattes) and the
   theses and dissertations aggregator repository (Oasisbr) is also
   detailed, culminating in the issuance of a certification seal.
   Conclusion: The results show that the adoption of these computational
   tools provides easy and agile access to an extensive set of consolidated
   information, previously dispersed across various sources, especially due
   to the diversity of repositories and individual access limitations.
   Thus, this study presents a set of computational tools whose
   functionalities are aligned with the guidelines of Open Science in
   Brazil.},
Publisher = {UNIV ESTADUAL CAMPINAS - SISTEMA BIBLIOTECAS},
Address = {Rua Sergio Buarque de Holanda, 421 - 1 andar - Biblioteca Central Cesar
   Lattes, Campinas, Sao Paulo, BRAZIL},
Type = {Article},
Language = {English},
Affiliation = {Silva, VD (Corresponding Author), Univ Passau, Passau, Germany.
   Silva, Vivian dos Santos; da Silva, Jesiel Viana, Univ Passau, Passau, Germany.
   Inst Fed Piaui, Teresina, PI, Brazil.
   Dias, Thiago Magela Rodrigues; Gabriel Junior, Rene Faustino, Ctr Fed Educ Tecnol Minas Gerais, Belo Horizonte, MG, Brazil.
   Univ Fed Rio Grande Do Sul, Porto Alegre, RS, Brazil.
   Segundo, Washington Luis Ribeiro de Carvalho, Inst Brasileiro Informac Ciencia \& Tecnol, Brasilia, DF, Brazil.},
DOI = {10.20396/rdbci.v21i00.8673171},
EISSN = {1678-765X},
Keywords = {Open science; Data repositories; Information processing; BrCris;
   Scientific data},
Keywords-Plus = {NETWORKS; GROWTH; IMPACT},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {vivian.ss@gmail.com
   jesiel.analista@gmail.com
   thiagomagela@gmail.com
   renefgj@gmail.com
   washingtonsegundo@ibict.br},
Affiliations = {University of Passau; Instituto Federal do Piaui (IFPI); Universidade
   Federal do Rio Grande do Sul},
Number-of-Cited-References = {23},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {RDBCI-Rev. Digital Biblioteconomia Ciencia Informacao},
Doc-Delivery-Number = {CT2D6},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001127416700002},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:001127416700001,
Author = {Silva, Vivian dos Santos and da Silva, Jesiel Viana and Dias, Thiago
   Magela Rodrigues and Gabriel Jr, Rene Faustino and Segundo, Washington
   Luis Ribeiro de Carvalho},
Title = {BrCris: tools for treatment, analysis, and dissemination of scientific
   information in support of Open Science in Brazil},
Journal = {RDBCI-REVISTA DIGITAL DE BIBLIOTECONOMIA E CIENCIA DA INFORMACAO},
Year = {2023},
Volume = {21},
Abstract = {Introduction: CRIS systems constitute comprehensive information systems
   over the entire ecosystem of the scientific process. BrCris aims to
   integrate and organize information regarding research activities,
   projects, publications, researchers, institutions, financing and other
   relevant data in the Brazilian scientific context. Objective: This study
   aims to discuss data processing on the BrCris Platform and analyze the
   computational tools used for this purpose, exploring three main
   approaches: data integration and consistency, visualization and
   validation, in addition to data certification. Methodology: The study is
   descriptive, presenting in detail the BrCris data processing steps,
   discussing the challenges encountered in handling large volumes of
   information. Furthermore, it describes the computational tools used to
   process scientific and technological information. Results: The study
   reveals the procedures for data processing and the computational tools
   developed for information systems, as well as the integration and
   analysis of the data obtained. The results of the processing and
   modeling of information based on VIVO, with data and graphic panels, and
   the opportunities for reusing the generated data are presented. The
   integration of data into a self-declared repository (Lattes) and the
   theses and dissertations aggregator repository (Oasisbr) is also
   detailed, culminating in the issuance of a certification seal.
   Conclusion: The results show that the adoption of these computational
   tools provides easy and agile access to an extensive set of consolidated
   information, previously dispersed across various sources, especially due
   to the diversity of repositories and individual access limitations.
   Thus, this study presents a set of computational tools whose
   functionalities are aligned with the guidelines of Open Science in
   Brazil.},
Publisher = {UNIV ESTADUAL CAMPINAS - SISTEMA BIBLIOTECAS},
Address = {Rua Sergio Buarque de Holanda, 421 - 1 andar - Biblioteca Central Cesar
   Lattes, Campinas, Sao Paulo, BRAZIL},
Type = {Article},
Language = {English},
Affiliation = {Silva, VD (Corresponding Author), Univ Passau, Passau, Germany.
   Silva, Vivian dos Santos, Univ Passau, Passau, Germany.
   da Silva, Jesiel Viana, Inst Fed Piaui, Teresina, PI, Brazil.
   Dias, Thiago Magela Rodrigues, Ctr Fed Educ Tecnol Minas Gerais, Belo Horizonte, MG, Brazil.
   Gabriel Jr, Rene Faustino, Univ Fed Rio Grande do Sul, Porto Alegre, RS, Brazil.
   Segundo, Washington Luis Ribeiro de Carvalho, Inst Brasileiro Informacao Ciencia \& Tecnol, Brasilia, DF, Brazil.},
DOI = {10.20396/rdbci.v21i00.8673171en},
Article-Number = {e023027},
EISSN = {1678-765X},
Keywords = {Open science; Data repositories; Information processing; BrCris;
   Scientific data},
Keywords-Plus = {NETWORKS; GROWTH; IMPACT},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {vivian.ss@gmail.com
   jesiel.analista@gmail.com
   thiagomagela@gmail.com
   renefgj@gmail.com
   washingtonsegundo@ibict.br},
Affiliations = {University of Passau; Instituto Federal do Piaui (IFPI); Universidade
   Federal do Rio Grande do Sul},
Number-of-Cited-References = {22},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {RDBCI-Rev. Digital Biblioteconomia Ciencia Informacao},
Doc-Delivery-Number = {CT2D6},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001127416700001},
DA = {2024-01-15},
}

@article{ WOS:000450172500002,
Author = {Cui, Licong and Zeng, Ningzhou and Kim, Matthew and Mueller, Remo and
   Hankosky, Emily R. and Redline, Susan and Zhang, Guo-Qiang},
Title = {X-search: an open access interface for cross-cohort exploration of the
   National Sleep Research Resource},
Journal = {BMC MEDICAL INFORMATICS AND DECISION MAKING},
Year = {2018},
Volume = {18},
Month = {NOV 13},
Abstract = {BackgroundThe National Sleep Research Resource (NSRR) is a large-scale,
   openly shared, data repository of de-identified, highly curated clinical
   sleep data from multiple NIH-funded epidemiological studies. Although
   many data repositories allow users to browse their content, few support
   fine-grained, cross-cohort query and exploration at study-subject level.
   We introduce a cross-cohort query and exploration system, called
   X-search, to enable researchers to query patient cohort counts across a
   growing number of completed, NIH-funded studies in NSRR and explore the
   feasibility or likelihood of reusing the data for research
   studies.MethodsX-search has been designed as a general framework with
   two loosely-coupled components: semantically annotated data repository
   and cross-cohort exploration engine. The semantically annotated data
   repository is comprised of a canonical data dictionary, data sources
   with a data dictionary, and mappings between each individual data
   dictionary and the canonical data dictionary. The cross-cohort
   exploration engine consists of five modules: query builder, graphical
   exploration, case-control exploration, query translation, and query
   execution. The canonical data dictionary serves as the unified metadata
   to drive the visual exploration interfaces and facilitate query
   translation through the mappings.ResultsX-search is publicly available
   at https://www.x-search.net/with nine NSRR datasets consisting of over
   26,000 unique subjects. The canonical data dictionary contains over 900
   common data elements across the datasets. X-search has received over
   1800 cross-cohort queries by users from 16 countries.ConclusionsX-search
   provides a powerful cross-cohort exploration interface for querying and
   exploring heterogeneous datasets in the NSRR data repository, so as to
   enable researchers to evaluate the feasibility of potential research
   studies and generate potential hypotheses using the NSRR data.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Cui, LC (Corresponding Author), Univ Kentucky, Dept Comp Sci, Lexington, KY 40506 USA.
   Cui, LC (Corresponding Author), Univ Kentucky, Inst Biomed Informat, Lexington, KY USA.
   Cui, Licong; Zeng, Ningzhou; Zhang, Guo-Qiang, Univ Kentucky, Dept Comp Sci, Lexington, KY 40506 USA.
   Cui, Licong; Zeng, Ningzhou; Hankosky, Emily R.; Zhang, Guo-Qiang, Univ Kentucky, Inst Biomed Informat, Lexington, KY USA.
   Kim, Matthew; Mueller, Remo; Redline, Susan, Brigham \& Womens Hosp, 75 Francis St, Boston, MA 02115 USA.
   Kim, Matthew; Mueller, Remo; Redline, Susan, Harvard Univ, Harvard Med Sch, Boston, MA 02115 USA.},
DOI = {10.1186/s12911-018-0682-y},
Article-Number = {99},
EISSN = {1472-6947},
Keywords = {Open access; FAIR; Cohort discovery; Hypothesis generation; Data
   heterogeneity; Data harmonization},
Keywords-Plus = {APNEA},
Research-Areas = {Medical Informatics},
Web-of-Science-Categories  = {Medical Informatics},
Author-Email = {licong.cui@uky.edu},
Affiliations = {University of Kentucky; University of Kentucky; Harvard University;
   Brigham \& Women's Hospital; Harvard University; Harvard Medical School},
Funding-Acknowledgement = {NIH National Heart, Lung, and Blood Institute {[}R24HL114473]; National
   Center for Advancing Translational Sciences {[}UL1TR001998]; National
   Institute on Drug Abuse {[}T32DA016176]; National Science Foundation
   (NSF) {[}1626364]; Office of Advanced Cyberinfrastructure (OAC); Direct
   For Computer \& Info Scie \& Enginr {[}1626364] Funding Source: National
   Science Foundation},
Funding-Text = {This work was supported by the NIH National Heart, Lung, and Blood
   Institute through grant number R24HL114473, National Center for
   Advancing Translational Sciences through grant number UL1TR001998,
   National Institute on Drug Abuse through grant number T32DA016176, and
   National Science Foundation (NSF) through grant number 1626364.
   Publication of this article was supported by grant R24HL114473. The
   content is solely the responsibility of the authors and does not
   necessarily represent the official views of the NIH or NSF.},
Number-of-Cited-References = {22},
Times-Cited = {9},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {7},
Journal-ISO = {BMC Med. Inform. Decis. Mak.},
Doc-Delivery-Number = {HA3RN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000450172500002},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000209190300003,
Author = {Piwowar, Heather A. and Vision, Todd J.},
Title = {Data reuse and the open data citation advantage},
Journal = {PEERJ},
Year = {2013},
Volume = {1},
Month = {OCT 1},
Abstract = {Background. Attribution to the original contributor upon reuse of
   published data is important both as a reward for data creators and to
   document the provenance of research findings. Previous studies have
   found that papers with publicly available datasets receive a higher
   number of citations than similar studies without available data.
   However, few previous analyses have had the statistical power to control
   for the many variables known to predict citation rate, which has led to
   uncertain estimates of the ``citation benefit{''}. Furthermore, little
   is known about patterns in data reuse over time and across datasets.
   Method and Results. Here, we look at citation rates while controlling
   for many known citation predictors and investigate the variability of
   data reuse. In a multivariate regression on 10,555 studies that created
   gene expression microarray data, we found that studies that made data
   available in a public repository received 9\% (95\% confidence interval:
   5\% to 13\%) more citations than similar studies for which the data was
   not made available. Date of publication, journal impact factor, open
   access status, number of authors, first and last author publication
   history, corresponding author country, institution citation history, and
   study topic were included as covariates. The citation benefit varied
   with date of dataset deposition: a citation benefit was most clear for
   papers published in 2004 and 2005, at about 30\%. Authors published most
   papers using their own datasets within two years of their first
   publication on the dataset, whereas data reuse papers published by
   third-party investigators continued to accumulate for at least six
   years. To study patterns of data reuse directly, we compiled 9,724
   instances of third party data reuse via mention of GEO or ArrayExpress
   accession numbers in the full text of papers. The level of third-party
   data use was high: for 100 datasets deposited in year 0, we estimated
   that 40 papers in PubMed reused a dataset by year 2, 100 by year 4, and
   more than 150 data reuse papers had been published by year 5. Data reuse
   was distributed across a broad base of datasets: a very conservative
   estimate found that 20\% of the datasets deposited between 2003 and 2007
   had been reused at least once by third parties.
   Conclusion. After accounting for other factors affecting citation rate,
   we find a robust citation benefit from open data, although a smaller one
   than previously reported. We conclude there is a direct effect of
   third-party data reuse that persists for years beyond the time when
   researchers have published most of the papers reusing their own data.
   Other factors that may also contribute to the citation benefit are
   considered. We further conclude that, at least for gene expression
   microarray data, a substantial fraction of archived datasets are reused,
   and that the intensity of dataset reuse has been steadily increasing
   since 2003.},
Publisher = {PEERJ INC},
Address = {341-345 OLD ST, THIRD FLR, LONDON, EC1V 9LL, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Piwowar, HA (Corresponding Author), Natl Evolutionary Synth Ctr, Durham, NC 27705 USA.
   Piwowar, Heather A.; Vision, Todd J., Natl Evolutionary Synth Ctr, Durham, NC 27705 USA.
   Piwowar, Heather A.; Vision, Todd J., Duke Univ, Dept Biol, Durham, NC USA.
   Vision, Todd J., Univ N Carolina, Dept Biol, Chapel Hill, NC USA.},
DOI = {10.7717/peerj.175},
Article-Number = {e175},
ISSN = {2167-8359},
Keywords = {Data reuse; Data repositories; Gene expression microarray; Incentives;
   Data archiving; Open data; Bibliometrics; Information science},
Keywords-Plus = {EXPRESSION; IMPACT},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {hpiwowar@gmail.com},
Affiliations = {The National Evolutionary Synthesis Center; Duke University; University
   of North Carolina; University of North Carolina Chapel Hill},
ResearcherID-Numbers = {Piwowar, Heather A/A-4680-2009},
Funding-Acknowledgement = {DataONE {[}OCI-0830944]; Dryad {[}DBI-0743720]; Discovery grant from the
   Natural Sciences and Engineering Research Council of Canada; Direct For
   Biological Sciences; Div Of Biological Infrastructure {[}0743720]
   Funding Source: National Science Foundation; Direct For Computer \& Info
   Scie \& Enginr; Office of Advanced Cyberinfrastructure (OAC) {[}0830944]
   Funding Source: National Science Foundation},
Funding-Text = {This study was funded by DataONE (OCI-0830944), Dryad (DBI-0743720), and
   a Discovery grant to Michael Whitlock from the Natural Sciences and
   Engineering Research Council of Canada. The funders had no role in study
   design, data collection and analysis, decision to publish, or
   preparation of the manuscript.},
Number-of-Cited-References = {33},
Times-Cited = {179},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {151},
Journal-ISO = {PeerJ},
Doc-Delivery-Number = {V36CF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000209190300003},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000402417200003,
Author = {Machova, Renata and Lnenicka, Martin},
Title = {Evaluating the Quality of Open Data Portals on the National Level},
Journal = {JOURNAL OF THEORETICAL AND APPLIED ELECTRONIC COMMERCE RESEARCH},
Year = {2017},
Volume = {12},
Number = {1},
Pages = {21-41},
Month = {JAN},
Abstract = {Over the last few years, governments worldwide have started to develop
   and implement open data initiatives to enable the release of government
   data in open and reusable formats without restriction or charge for
   their use by society. As a result, a large number of open data
   repositories, catalogues and portals have been emerging in the world.
   The efficient development of open data portals makes it necessary to
   evaluate their quality systematic, in order to understand them better
   and assess the various types of value they generate. Citizens also
   expect data disclosed by official authorities to have quality in the
   sense that they are official data and therefore should be accurate and
   reliable. Consequently, the aim of this paper is to examine and compare
   the quality of these portals. For this purpose, a benchmarking framework
   is proposed and validated to evaluate the quality of open data portals
   on the national level. The results obtained show that the number of
   datasets online and the sophistication of open data portals and their
   functions differ, reflecting the lack of harmonization and the need for
   quality standards. In particular, the United Kingdom, India and the
   United States have published many datasets and launched advanced
   portals.},
Publisher = {UNIV TALCA, FAC INGENIERIA},
Address = {MERCED 437, CURICO, 00000, CHILE},
Type = {Article},
Language = {English},
Affiliation = {Máchová, R (Corresponding Author), Univ Pardubice, Fac Econ \& Adm, Pardubice, Czech Republic.
   Machova, Renata; Lnenicka, Martin, Univ Pardubice, Fac Econ \& Adm, Pardubice, Czech Republic.},
DOI = {10.4067/S0718-18762017000100003},
ISSN = {0718-1876},
Keywords = {Open data; Open government; National open data portals; Benchmarking
   framework; Content analysis; Evaluation; Quality},
Keywords-Plus = {BIG DATA; MODEL},
Research-Areas = {Business \& Economics},
Web-of-Science-Categories  = {Business},
Author-Email = {renata.machova@upce.cz
   martin.lnenicka@student.upce.cz},
Affiliations = {University of Pardubice},
ResearcherID-Numbers = {Lněnička, Martin/V-3049-2019},
ORCID-Numbers = {Lněnička, Martin/0000-0002-3720-8935},
Funding-Acknowledgement = {University of Pardubice {[}SGS\_2016\_023]},
Funding-Text = {The authors would like to thank the reviewers for taking the time to
   assess this paper and for providing valuable critique which helped to
   improve this paper. The authors would like to acknowledge the assistance
   of the Student Grant Competition of the University of Pardubice No.
   SGS\_2016\_023.},
Number-of-Cited-References = {58},
Times-Cited = {62},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {68},
Journal-ISO = {J. Theor. Appl. Electron. Commer. Res.},
Doc-Delivery-Number = {EW3QU},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000402417200003},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000433205600003,
Author = {Harper, Lindsey M. and Kim, Youngseek},
Title = {Attitudinal, normative, and resource factors affecting psychologists'
   intentions to adopt an open data badge: An empirical analysis},
Journal = {INTERNATIONAL JOURNAL OF INFORMATION MANAGEMENT},
Year = {2018},
Volume = {41},
Pages = {23-32},
Month = {AUG},
Abstract = {The purpose of this research is to investigate the attitudinal,
   normative, and resource factors affecting psychologists' adoption of an
   open data badge. The theory of planned behavior was employed to
   demonstrate how these factors influence behavioral intentions to adopt
   an open data badge. This research used a survey method to examine to
   what extent those attitudinal, normative, resource factors influence
   psychologists' behavioral intentions to adopt an open data badge, and
   therefore engage in data sharing behaviors. A national survey (n= 341)
   across the field of psychology showed that perceived benefit and
   perceived risk had significant positive and negative relationships with
   attitude toward the open data badge respectively. Furthermore, attitude
   toward open data badge and norm of data sharing had significant positive
   influences on psychologists' behavioral intentions to adopt the open
   data badge. Perceived effort had a significant negative relationship
   with the behavioral intention to adopt the open data badge, but had no
   effect toward attitudes surrounding the badge. However, this research
   found that the availability of a data repository and pressure from an
   open science journal did not have any significant relationship with
   behavioral intention to adopt the open data badge. The discussion
   includes implications for psychologists from both practical and
   theoretical perspectives. Additionally, future directions for gauging
   psychologists' adoption of the open data badge and increasing data
   sharing behaviors are discussed.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Kim, Y (Corresponding Author), Univ Kentucky, Sch Informat Sci, 331 Little Lib Bldg, Lexington, KY 40506 USA.
   Harper, Lindsey M., Marshall Univ, Libraries \& Online Learning, One John Marshall Dr, Huntington, WV 25755 USA.
   Kim, Youngseek, Univ Kentucky, Sch Informat Sci, 331 Little Lib Bldg, Lexington, KY 40506 USA.},
DOI = {10.1016/j.ijinfomgt.2018.03.001},
ISSN = {0268-4012},
EISSN = {1873-4707},
Keywords = {Open data badge; Data sharing; Psychologist; Psychology; Theory of
   planned behavior},
Keywords-Plus = {DATA SHARING BEHAVIORS; USER ACCEPTANCE; DATA CURATION; KNOWLEDGE;
   REPOSITORIES; ROLES; TECHNOLOGY; BUSINESS; SCIENCE; ISSUES},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {harper166@marshall.edu
   youngseek.kim@uky.edu},
Affiliations = {Marshall University; University of Kentucky},
ORCID-Numbers = {Harper, Lindsey/0000-0001-5065-4502},
Number-of-Cited-References = {61},
Times-Cited = {16},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {67},
Journal-ISO = {Int. J. Inf. Manage.},
Doc-Delivery-Number = {GH2BC},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000433205600003},
DA = {2024-01-15},
}

@article{ WOS:000475287900008,
Author = {Scherer, David and Valen, Daniel},
Title = {Balancing Multiple Roles of Repositories: Developing a Comprehensive
   Repository at Carnegie Mellon University},
Journal = {PUBLICATIONS},
Year = {2019},
Volume = {7},
Number = {2},
Month = {JUN},
Abstract = {Many academic and research institutions today maintain multiple types of
   institutional repositories operating on different systems and platforms
   to accommodate the needs and governance of the materials they house.
   Often, these institutions support multiple repository infrastructures,
   as these systems and platforms are not able to accommodate the broad
   range of materials that an institution creates. Announced in 2017, the
   Carnegie Mellon University (CMU) Libraries implemented a new repository
   solution and service model. Built upon the Figshare for Institutions
   platform, the KiltHub repository has taken on the role of a traditional
   institutional repository and institutional data repository, meeting the
   disparate needs of its researchers, faculty, and students. This paper
   will review how the CMU Libraries implemented the KiltHub repository and
   how the repository services was redeveloped to provide a more
   encompassing solution for traditional institutional repository materials
   and research datasets. Additionally, this paper will summarize how the
   CMU University Libraries surveyed the current repository landscape,
   decided to implement Figshare for Institutions as a comprehensive
   institutional repository, revised its previous repository service model
   to accommodate the influx of new material types, and what needed to be
   developed for campus engagement. This paper is based upon a presentation
   of the same title delivered at the 2018 Open Repositories Conference
   held at Montana State University in Bozeman, Montana.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Scherer, D (Corresponding Author), Carnegie Mellon Univ, Univ Lib, Pittsburgh, PA 15237 USA.
   Scherer, David, Carnegie Mellon Univ, Univ Lib, Pittsburgh, PA 15237 USA.
   Valen, Daniel, Figshare, Cambridge, MA 02139 USA.},
DOI = {10.3390/publications7020030},
Article-Number = {30},
ISSN = {2304-6775},
Keywords = {institutional repositories; research data; Carnegie Mellon University;
   scholarly communications; open access; open scholarship; open science;
   open data; engagement},
Keywords-Plus = {INSTITUTIONAL REPOSITORIES; OPEN ACCESS; RESEARCH INFORMATION},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {daschere@andrew.cmu.edu
   dan@figshare.com},
Affiliations = {Carnegie Mellon University},
ResearcherID-Numbers = {Scherer, David A/L-5920-2016
   Scherer, David/JOK-8640-2023
   },
ORCID-Numbers = {Scherer, David A/0000-0002-6244-4331
   Valen, Daniel/0000-0002-9479-6438},
Number-of-Cited-References = {39},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {12},
Journal-ISO = {Publications},
Doc-Delivery-Number = {II6FG},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000475287900008},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000422820000006,
Author = {Herala, Antti and Kasurinen, Jussi and Vanhala, Erno},
Title = {Views on Open Data Business from Software Development Companies},
Journal = {JOURNAL OF THEORETICAL AND APPLIED ELECTRONIC COMMERCE RESEARCH},
Year = {2018},
Volume = {13},
Number = {1},
Pages = {91-105},
Month = {JAN},
Abstract = {The interest towards the concept of open data has increased during the
   last ten years, as governments and municipalities have decided to open
   their data repositories. This has led to a new generation of mobile
   apps, which utilize this data to improve the feature richness and the
   overall user experience for the customers. In this study, we interviewed
   representatives of five software organization and discussed their views
   towards opening data - private and public - and also using the open data
   in practice. Based on our observations, the companies see very limited
   scope for the use of open data as a business asset: the main
   applications seem to gravitate towards function as an additional feature
   for an existing product, not a source of new innovations or business
   ventures. The results also illustrate on how little benefit the
   organizations consider to gain from opening their private data, and what
   alternatives there are for sharing data in a profitable manner.
   Additionally, as based on the observations, a strategy classification on
   the different data sharing methods is formulated and presented.},
Publisher = {UNIV TALCA, FAC INGENIERIA},
Address = {MERCED 437, CURICO, 00000, CHILE},
Type = {Article},
Language = {English},
Affiliation = {Herala, A (Corresponding Author), Lappeenranta Univ Technol, Sch Business \& Management, Lappeenranta, Finland.
   Herala, Antti, Lappeenranta Univ Technol, Sch Business \& Management, Lappeenranta, Finland.
   Kasurinen, Jussi, Southern Eastern Finland Univ Appl Sci, Dept Digital Econ, Kotka, Finland.
   Vanhala, Erno, Univ Tampere, Dept IT Adm, Tampere, Finland.},
DOI = {10.4067/S0718-18762018000100106},
ISSN = {0718-1876},
Keywords = {Open data; Data business; Data management; Software development; Private
   data},
Research-Areas = {Business \& Economics},
Web-of-Science-Categories  = {Business},
Author-Email = {antti.herala@lut.fi
   jussi.kasurinen@xamk.fi
   erno.vanhala@staff.uta.fi},
Affiliations = {Lappeenranta-Lahti University of Technology LUT; South-Eastern Finland
   University of Applied Sciences; Tampere University},
ResearcherID-Numbers = {Kasurinen, Jussi P/B-5147-2015
   Vanhala, Erno/Q-2025-2019},
ORCID-Numbers = {Kasurinen, Jussi P/0000-0001-9454-8664
   Vanhala, Erno/0000-0001-9039-7731},
Funding-Acknowledgement = {Digital, Internet, Materials \& Engineering Co-Creation (DIMECC)},
Funding-Text = {The authors of this study would like to thank Digital, Internet,
   Materials \& Engineering Co-Creation (DIMECC) and their project, Service
   Solutions for Fleet Management (S4Fleet) for funding this study.},
Number-of-Cited-References = {36},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {14},
Journal-ISO = {J. Theor. Appl. Electron. Commer. Res.},
Doc-Delivery-Number = {FT0MM},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000422820000006},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000342807900009,
Author = {Janssen, Marijn and Zuiderwijk, Anneke},
Title = {Infomediary Business Models for Connecting Open Data Providers and Users},
Journal = {SOCIAL SCIENCE COMPUTER REVIEW},
Year = {2014},
Volume = {32},
Number = {5, SI},
Pages = {694-711},
Month = {OCT},
Abstract = {Many public organizations are opening their data to the general public
   and embracing social media in order to stimulate innovation. These
   developments have resulted in the rise of new, infomediary business
   models, positioned between open data providers and users. Yet the
   variation among types of infomediary business models is little
   understood. The aim of this article is to contribute to the
   understanding of the diversity of existing infomediary business models
   that are driven by open data and social media. Cases presenting
   different modes of open data utilization in the Netherlands are
   investigated and compared. Six types of business models are identified:
   single-purpose apps, interactive apps, information aggregators,
   comparison models, open data repositories, and service platforms. The
   investigated cases differ in their levels of access to raw data and in
   how much they stimulate dialogue between different stakeholders involved
   in open data publication and use. Apps often are easy to use and provide
   predefined views on data, whereas service platforms provide
   comprehensive functionality but are more difficult to use. In the
   various business models, social media is sometimes used for rating and
   discussion purposes, but it is rarely used for stimulating dialogue or
   as input to policy making. Hybrid business models were identified in
   which both public and private organizations contribute to value
   creation. Distinguishing between different types of open data users was
   found to be critical in explaining different business models.},
Publisher = {SAGE PUBLICATIONS INC},
Address = {2455 TELLER RD, THOUSAND OAKS, CA 91320 USA},
Type = {Article},
Language = {English},
Affiliation = {Janssen, M (Corresponding Author), Delft Univ Technol, Jaffalaan 5 Bldg 31,Room B3,150, NL-2628 BX Delft, Netherlands.
   Janssen, Marijn, Delft Univ Technol, Technol Policy \& Management Fac, NL-2628 BX Delft, Netherlands.
   Zuiderwijk, Anneke, Delft Univ Technol, Fac Technol Policy \& Management, ICT Sect, NL-2628 BX Delft, Netherlands.},
DOI = {10.1177/0894439314525902},
ISSN = {0894-4393},
EISSN = {1552-8286},
Keywords = {social media; infomediaries; intermediaries; open data; open data
   ecosystems; business models; apps; e-government; open government; web 2;
   0},
Keywords-Plus = {E-GOVERNMENT; INFORMATION; BENEFITS; BARRIERS; IMPACT},
Research-Areas = {Computer Science; Information Science \& Library Science; Social
   Sciences - Other Topics},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Information Science \&
   Library Science; Social Sciences, Interdisciplinary},
Author-Email = {m.f.w.h.a.janssen@tudelft.nl},
Affiliations = {Delft University of Technology; Delft University of Technology},
ResearcherID-Numbers = {Zuiderwijk, Anneke/AAQ-3370-2020
   Janssen, Marijn/H-6223-2013},
ORCID-Numbers = {Zuiderwijk, Anneke/0000-0002-3552-7289
   Janssen, Marijn/0000-0001-6211-8790},
Funding-Acknowledgement = {ENGAGE FP7 Infrastructure Project (An Infrastructure for Open, Linked
   Governmental Data Provision Towards Research Communities and Citizens)},
Funding-Text = {The authors disclosed receipt of the following financial support for the
   research, authorship, and/or publication of this article: This paper is
   related to the ENGAGE FP7 Infrastructure Project (An Infrastructure for
   Open, Linked Governmental Data Provision Towards Research Communities
   and Citizens), which started in June 2011. The authors would like to
   thank their colleagues of the ENGAGE project for their input toward this
   paper. The views expressed here are those of the authors and do not
   necessarily reflect the views of the project.},
Number-of-Cited-References = {52},
Times-Cited = {90},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {156},
Journal-ISO = {Soc. Sci. Comput. Rev.},
Doc-Delivery-Number = {AQ4YP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000342807900009},
DA = {2024-01-15},
}

@article{ WOS:000768058200001,
Author = {Poudel, Manoj and Sarode, Rashmi P. and Watanobe, Yutaka and Mozgovoy,
   Maxim and Bhalla, Subhash},
Title = {Processing Analytical Queries over Polystore System for a Large
   Astronomy Data Repository},
Journal = {APPLIED SCIENCES-BASEL},
Year = {2022},
Volume = {12},
Number = {5},
Month = {MAR},
Abstract = {There are extremely large heterogeneous databases in the astronomical
   data domain, which keep increasing in size. The data types vary from
   images of astronomical objects to unstructured texts, relations, and
   key-values. Many astronomical data repositories manage such kinds of
   data. The Zwicky Transient Facility (ZTF) is one such data repository
   with a large amount of data with different varieties. Handling different
   types of data in a single database may have performance and efficiency
   issues. In this study, we propose a web-based query system built around
   the Polystore database architecture, and attempt to provide a solution
   for the growing size of data in the astronomical domain. The proposed
   system will unify querying over multiple datasets directly, thereby
   eliminating the effort to translate complex queries and simplify the
   work for the users in the astronomical domain. In this proposal, we
   study the models of data integration, analyze them, and incorporate them
   into a system to manage linked open data provided by astronomical
   domain. The proposed system is scalable, and its model can be used for
   various other systems to efficiently manage heterogeneous data.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Poudel, M; Sarode, RP (Corresponding Author), Univ Aizu, Grad Dept Comp \& Informat Syst, Aizu Wakamatsu, Fukushima 9658580, Japan.
   Poudel, Manoj; Sarode, Rashmi P.; Watanobe, Yutaka; Mozgovoy, Maxim; Bhalla, Subhash, Univ Aizu, Grad Dept Comp \& Informat Syst, Aizu Wakamatsu, Fukushima 9658580, Japan.},
DOI = {10.3390/app12052663},
Article-Number = {2663},
EISSN = {2076-3417},
Keywords = {ZTF data; PTF data; Polystore; link data; data integration},
Research-Areas = {Chemistry; Engineering; Materials Science; Physics},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary; Engineering, Multidisciplinary; Materials
   Science, Multidisciplinary; Physics, Applied},
Author-Email = {d8212102@u-aizu.ac.jp
   rashmipsarode@gmail.com
   yutaka@u-aizu.ac.jp
   mozgovoy@u-aizu.ac.jp
   c21bhala@u-aizu.ac.jp},
Affiliations = {University of Aizu},
ResearcherID-Numbers = {Sarode, Rashmi Prabhakar/AHA-2693-2022
   },
ORCID-Numbers = {Mozgovoy, Maxim/0000-0003-0684-4012
   Poudel, Manoj/0000-0002-2693-2004},
Number-of-Cited-References = {46},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Appl. Sci.-Basel},
Doc-Delivery-Number = {ZR8WO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000768058200001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000298841000004,
Author = {Kinsinger, Christopher R. and Apffel, James and Baker, Mark and Bian,
   Xiaopeng and Borchers, Christoph H. and Bradshaw, Ralph and Brusniak,
   Mi-Youn and Chan, Daniel W. and Deutsch, Eric W. and Domon, Bruno and
   Gorman, Jeff and Grimm, Rudolf and Hancock, William and Hermjakob,
   Henning and Horn, David and Hunter, Christie and Kolar, Patrik and
   Kraus, Hans-Joachim and Langen, Hanno and Linding, Rune and Moritz,
   Robert L. and Omenn, Gilbert S. and Orlando, Ron and Pandey, Akhilesh
   and Ping, Peipei and Rahbar, Amir and Rivers, Robert and Seymour, Sean
   L. and Simpson, Richard J. and Slotta, Douglas and Smith, Richard D. and
   Stein, Stephen E. and Tabb, David L. and Tagle, Danilo and Yates, John
   R. and Rodriguez, Henry},
Title = {Recommendations for mass spectrometry data quality metrics for open
   access data (corollary to the Amsterdam principles)},
Journal = {PROTEOMICS},
Year = {2012},
Volume = {12},
Number = {1},
Pages = {11-20},
Month = {JAN},
Abstract = {Policies supporting the rapid and open sharing of proteomic data are
   being implemented by the leading journals in the field. The proteomics
   community is taking steps to ensure that data are made publicly
   accessible and are of high quality, a challenging task that requires the
   development and deployment of methods for measuring and documenting data
   quality metrics. On September 18, 2010, the U.S. National Cancer
   Institute (NCI) convened the International Workshop on Proteomic Data
   Quality Metrics in Sydney, Australia, to identify and address issues
   facing the development and use of such methods for open access
   proteomics data. The stakeholders at the workshop enumerated the key
   principles underlying a framework for data quality assessment in mass
   spectrometry data that will meet the needs of the research community,
   journals, funding agencies, and data repositories. Attendees discussed
   and agreed upon two primary needs for the wide use of quality metrics:
   (i) an evolving list of comprehensive quality metrics and (ii) standards
   accompanied by software analytics. Attendees stressed the importance of
   increased education and training programs to promote reliable protocols
   in proteomics. This workshop report explores the historic precedents,
   key discussions, and necessary next steps to enhance the quality of open
   access data. By agreement, this article is published simultaneously in
   Proteomics, Proteomics Clinical Applications, Journal of Proteome
   Research, and Molecular and Cellular Proteomics, as a public service to
   the research community. The peer review process was a coordinated effort
   conducted by a panel of referees selected by the journals.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Kinsinger, CR (Corresponding Author), NCI, Off Canc Clin Prote Res, NIH, 31 Ctr Dr,MSC 2580, Bethesda, MD 20892 USA.
   Kinsinger, Christopher R.; Rahbar, Amir; Rodriguez, Henry, NCI, Off Canc Clin Prote Res, NIH, Bethesda, MD 20892 USA.
   Apffel, James, Agilent Res Labs, Santa Clara, CA USA.
   Baker, Mark, Macquarie Univ, Dept Chem \& Biomol Sci, Sydney, NSW 2109, Australia.
   Bian, Xiaopeng, NCI, Ctr Bioinformat \& Informat Technol, NIH, Bethesda, MD 20892 USA.
   Borchers, Christoph H., Univ Victoria, Genome BC Prote Ctr, Victoria, BC, Canada.
   Bradshaw, Ralph, Univ Calif San Francisco, Mass Spectrometry Facil, San Francisco, CA 94143 USA.
   Chan, Daniel W., Johns Hopkins Univ, Sch Med, Dept Pathol, Baltimore, MD 21205 USA.
   Domon, Bruno, CRP Sante, Luxembourg Clin Prote Ctr, Luxembourg, Luxembourg.
   Gorman, Jeff, Queensland Inst Med Res, Prot Discovery Ctr, Herston, Qld 4006, Australia.
   Grimm, Rudolf, Agilent Technol, Santa Clara, CA USA.
   Hancock, William, Northeastern Univ, Dept Chem \& Chem Biol, Boston, MA 02115 USA.
   Hermjakob, Henning, European Bioinformat Inst, Prote Serv, Cambridge, England.
   Horn, David, Thermo Fisher Sci, Prote Software Strateg Mkt, San Jose, CA USA.
   Hunter, Christie; Rivers, Robert, AB SCIEX, Foster City, AB, Canada.
   Kolar, Patrik, European Commiss, Directorate Gen Res, Brussels, Belgium.
   Kraus, Hans-Joachim, Wiley VCH, Weinheim, Germany.
   Langen, Hanno, Hoffmann La Roche Ag, Exploratory Biomarkers, CH-4002 Basel, Switzerland.
   Linding, Rune, Tech Univ Denmark DTU, Cellular Signal Integrat Grp C SIG, Ctr Biol Sequence Anal CBS, Dept Syst Biol, Lyngby, Denmark.
   Moritz, Robert L., Inst Syst Biol, Cellular \& Mol Logic Unit, Seattle, WA USA.
   Omenn, Gilbert S., Univ Michigan, Ctr Computat Med \& Bioinformat, Ann Arbor, MI 48109 USA.
   Orlando, Ron, Univ Georgia, Complex Carbohydrate Res Ctr, Athens, GA 30602 USA.
   Pandey, Akhilesh, Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD USA.
   Ping, Peipei, Univ Calif Los Angeles, David Geffen Sch Med, Los Angeles, CA 90095 USA.
   Seymour, Sean L., NCI, Small Business Dev Ctr, NIH, Bethesda, MD 20892 USA.
   Simpson, Richard J., La Trobe Univ, La Trobe Inst Mol Sci, Bundoora, Vic, Australia.
   Slotta, Douglas, NIH, Ctr Biotechnol Informat, Bethesda, MD 20892 USA.
   Smith, Richard D., Pacific NW Natl Lab, Richland, WA 99352 USA.
   Stein, Stephen E., NIST, Chem Reference Data Grp, Gaithersburg, MD 20899 USA.
   Tabb, David L., Vanderbilt Ingram Canc Ctr, Nashville, TN USA.
   Tagle, Danilo, Natl Inst Neurol Disorders \& Stroke, NIH, Bethesda, MD USA.
   Yates, John R., Scripps Res Inst, La Jolla, CA 92037 USA.},
DOI = {10.1002/pmic.201100562},
ISSN = {1615-9853},
EISSN = {1615-9861},
Keywords = {Amsterdam principles; Bioinformatics; Data quality; Metrics; Open
   access; Selected reaction monitoring; Standards},
Keywords-Plus = {PROTEIN IDENTIFICATION DATA; PEPTIDE IDENTIFICATION; CLINICAL
   PROTEOMICS; MINIMUM INFORMATION; STATISTICAL-MODEL; GUIDELINES;
   RESOURCE; REPRODUCIBILITY; PERFORMANCE; VALIDATION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
Author-Email = {kinsingc@mail.nih.gov},
Affiliations = {National Institutes of Health (NIH) - USA; NIH National Cancer Institute
   (NCI); Agilent Technologies; Macquarie University; National Institutes
   of Health (NIH) - USA; NIH National Cancer Institute (NCI); University
   of Victoria; University of California System; University of California
   San Francisco; Johns Hopkins University; Luxembourg Institute of Health;
   QIMR Berghofer Medical Research Institute; Agilent Technologies;
   Northeastern University; European Molecular Biology Laboratory (EMBL);
   Thermo Fisher Scientific; Roche Holding; Technical University of
   Denmark; Institute for Systems Biology (ISB); University of Michigan
   System; University of Michigan; University System of Georgia; University
   of Georgia; Johns Hopkins University; University of California System;
   University of California Los Angeles; University of California Los
   Angeles Medical Center; David Geffen School of Medicine at UCLA;
   National Institutes of Health (NIH) - USA; NIH National Cancer Institute
   (NCI); La Trobe University; National Institutes of Health (NIH) - USA;
   United States Department of Energy (DOE); Pacific Northwest National
   Laboratory; National Institute of Standards \& Technology (NIST) - USA;
   Vanderbilt University; National Institutes of Health (NIH) - USA; NIH
   National Institute of Neurological Disorders \& Stroke (NINDS); Scripps
   Research Institute},
ResearcherID-Numbers = {Smith, Richard/HMD-4857-2023
   Moritz, Robert L/B-9222-2011
   Deutsch, Eric/AAF-5912-2020
   Hermjakob, Henning/AFM-3497-2022
   Pandey, Akhilesh/B-4127-2009
   BORCHERS, Christoph/U-5964-2019
   Simpson, Richard/A-6947-2012
   Bradshaw, Ralph A/K-1515-2013
   Smith, Richard D/J-3664-2012
   },
ORCID-Numbers = {Hermjakob, Henning/0000-0001-8479-0262
   Pandey, Akhilesh/0000-0001-9943-6127
   Smith, Richard D/0000-0002-2381-2349
   Ping, Peipei/0000-0003-3583-3881
   Simpson, Richard/0000-0002-9834-0796
   Tabb, David/0000-0001-7223-578X
   Deutsch, Eric/0000-0001-8732-0928
   Baker, Mark/0000-0001-5858-4035
   Omenn, Gilbert S./0000-0002-8976-6074},
Number-of-Cited-References = {51},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {42},
Journal-ISO = {Proteomics},
Doc-Delivery-Number = {872WL},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000298841000004},
OA = {Green Submitted, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000906908100011,
Author = {Stefanidis, Konstantinos and Varlas, George and Papaioannou, George and
   Papadopoulos, Anastasios and Dimitriou, Elias},
Title = {Assessing temporal variability of lake turbidity and trophic state of
   European lakes using open data repositories},
Journal = {SCIENCE OF THE TOTAL ENVIRONMENT},
Year = {2023},
Volume = {857},
Number = {3},
Month = {JAN 20},
Abstract = {Water turbidity is one of the more important water quality parameters
   that is strictly linked with the productivity of the lake and is
   commonly used as an indicator of the trophic state. However, limited
   field data availability across wide geo-graphic gradients may hinder the
   conduction of large scale longitudinal studies. In this study, time
   series of lake tur-bidity and trophic state index (TSI) between 2002 and
   2012 were obtained from the Copernicus Lake Water products to create a
   large longitudinal dataset of lake variables for 22 European lakes. The
   dataset was combined with estimates of nutrient concentrations and
   surface water temperature obtained from the Hydrological Predictions for
   the Environment (HYPE) and ERA5-Land data repositories, that were used
   as environmental predictors. Hence, the validity of the lake water
   quality parameters was tested by a) exploring their spatial and temporal
   variability and b) identifying associations with the environmental
   predictors. For this purpose, seasonal Mann-Kendall tests were applied
   to find significant inter-annual trends of turbidity and TSI for each
   lake, and generalized additive models (GAMs) were employed to identify
   the main parameters that shape their temporal dynamics. Although we did
   not find significant inter-annual changes, our findings highlighted the
   strong influence of seasonality and surface water temper-ature in
   defining the temporal variability patterns in most of the lakes. In
   addition, the importance of nutrients varied among lakes as several
   lakes exhibited narrow nutrient gradients reflecting relatively stable
   nutrient conditions during the examined period. Other lake intrinsic
   factors, such as local climate and biotic interactions, are important
   drivers of shaping turbidity and nutrient dynamics. This study
   highlighted the usefulness of combining lake data from large
   repositories in conducting large scale spatial studies as a valuable
   asset for future lake research and management purposes.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Stefanidis, K (Corresponding Author), Inst Marine Biol Resources \& Inland Waters, Hellen Ctr Marine Res, 46-7 Km Athens Sounio Ave, Anavyssos 19013, Attica, Greece.
   Stefanidis, Konstantinos; Varlas, George; Papaioannou, George; Papadopoulos, Anastasios; Dimitriou, Elias, Inst Marine Biol Resources \& Inland Waters, Hellen Ctr Marine Res, 46-7 Km Athens Sounio Ave, Anavyssos 19013, Attica, Greece.
   Stefanidis, Konstantinos, Univ Patras, Dept Biol, Univ Campus Rio, GR-26500 Patras, Greece.
   Papaioannou, George, Democritus Univ Thrace, Dept Forestry \& Management Environm \& Nat Resource, Orestiada 68200, Greece.},
DOI = {10.1016/j.scitotenv.2022.159618},
EarlyAccessDate = {OCT 2022},
Article-Number = {159618},
ISSN = {0048-9697},
EISSN = {1879-1026},
Keywords = {Lakes; Eutrophication; Turbidity; Trophic state index; Generalized
   additive models; ERA5-land},
Keywords-Plus = {WATER-QUALITY; CLIMATE-CHANGE; FRESH-WATER; SHALLOW LAKES;
   PHYTOPLANKTON; DYNAMICS; EUTROPHICATION; IMPACTS; WIND},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Environmental Sciences},
Author-Email = {kstefanidis@hcmr.gr},
Affiliations = {Hellenic Centre for Marine Research; University of Patras; Democritus
   University of Thrace},
ResearcherID-Numbers = {Stefanidis, Kostas/H-7262-2019
   Papaioannou, George/K-2683-2019
   Varlas, George/L-8082-2019
   Papadopoulos, Anastasios/L-6578-2013},
ORCID-Numbers = {Stefanidis, Kostas/0000-0002-9121-3188
   Papaioannou, George/0000-0002-7389-6640
   Varlas, George/0000-0001-7929-9452
   Papadopoulos, Anastasios/0000-0002-4441-3443},
Number-of-Cited-References = {71},
Times-Cited = {1},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {21},
Journal-ISO = {Sci. Total Environ.},
Doc-Delivery-Number = {7M8NM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000906908100011},
DA = {2024-01-15},
}

@article{ WOS:000300458300077,
Author = {Kinsinger, Christopher R. and Apffel, James and Baker, Mark and Bian,
   Xiaopeng and Borchers, Christoph H. and Bradshaw, Ralph and Brusniak,
   Mi-Youn and Chan, Daniel W. and Deutsch, Eric W. and Domon, Bruno and
   Gorman, Jeff and Grimm, Rudolf and Hancock, William and Hermjakob,
   Henning and Horn, David and Hunter, Christie and Kolar, Patrik and
   Kraus, Hans-Joachim and Langen, Hanno and Linding, Rune and Moritz,
   Robert L. and Omenn, Gilbert S. and Orlando, Ron and Pandey, Akhilesh
   and Ping, Peipei and Rahbar, Amir and Rivers, Robert and Seymour, Sean
   L. and Simpson, Richard J. and Slotta, Douglas and Smith, Richard D. and
   Stein, Stephen E. and Tabb, David L. and Tagle, Danilo and Yates, III,
   John R. and Rodriguez, Henry},
Title = {Recommendations for Mass Spectrometry Data Quality Metrics for Open
   Access Data (Corollary to the Amsterdam Principles)},
Journal = {JOURNAL OF PROTEOME RESEARCH},
Year = {2012},
Volume = {11},
Number = {2},
Pages = {1412-1419},
Month = {FEB},
Abstract = {Policies supporting the rapid and open sharing of proteomic data are
   being implemented by the leading journals in the field. The proteomics
   community is taking steps to ensure that data are made publicly
   accessible and are of high quality, a challenging task that requires the
   development and deployment of methods for measuring and documenting data
   quality metrics. On September 18, 2010, the U.S. National Cancer
   Institute (NCI) convened the ``International Workshop on Proteomic Data
   Quality Metrics{''} in Sydney, Australia, to identify and address issues
   facing the development and use of such methods for open access
   proteomics data. The stakeholders at the workshop enumerated the key
   principles underlying a framework for data quality assessment in mass
   spectrometry data that will meet the needs of the research community,
   journals, funding agencies, and data repositories. Attendees discussed
   and agreed up on two primary needs for the wide use of quality metrics:
   (1) an evolving list of comprehensive quality metrics and (2) standards
   accompanied by software analytics. Attendees stressed the importance of
   increased education and training programs to promote reliable protocols
   in proteomics. This workshop report explores the historic precedents,
   key discussions, and necessary next steps to enhance the quality of open
   access data. By agreement, this article is published simultaneously in
   the Journal of Proteome Research, Molecular and Cellular Proteomics,
   Proteomics, and Proteomics Clinical Applications as a public service to
   the research community. The peer review process was a coordinated effort
   conducted by a panel of referees selected by the journals.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Kinsinger, CR (Corresponding Author), NCI, Off Canc Clin Prote Res, NIH, 31 Ctr Dr,MSC 2580, Bethesda, MD 20892 USA.
   Kinsinger, Christopher R., NCI, Off Canc Clin Prote Res, NIH, Bethesda, MD 20892 USA.
   Agilent Res Labs, Santa Clara, CA 95051 USA.
   Macquarie Univ, Dept Chem \& Biomol Sci, Sydney, NSW 2109, Australia.
   NCI, Ctr Bioinformat \& Informat Technol, NIH, Bethesda, MD 20892 USA.
   Univ Victoria, Genome BC Prote Ctr, Victoria, BC V8Z 7X8, Canada.
   Univ Calif San Francisco, Mass Spectrometry Facil, San Francisco, CA 94143 USA.
   Inst Syst Biol, Seattle, WA 98103 USA.
   Johns Hopkins Univ, Sch Med, Dept Pathol, Baltimore, MD 21231 USA.
   Inst Syst Biol, Seattle, WA 98109 USA.
   CRP Sante, Luxembourg Clin Prote Ctr, L-1445 Strassen, Luxembourg.
   Queensland Inst Med Res, Prot Discovery Ctr, Herston, Qld 4029, Australia.
   Agilent Technol, Santa Clara, CA 95051 USA.
   Northeastern Univ, Dept Chem \& Chem Biol, Boston, MA 02115 USA.
   European Bioinformat Inst, Prote Serv, Cambridge CB10 1SD, England.
   Thermo Fisher Sci, Prote Software Strateg Mkt, San Jose, CA 95134 USA.
   AB SCIEX, Foster City, CA 94404 USA.
   Commiss European Communities, Directorate Gen Res, B-1049 Brussels, Belgium.
   Wiley VCH, D-69469 Weinheim, Germany.
   Hoffmann La Roche AG, Exploratory Biomarkers, CH-4070 Basel, Switzerland.
   Tech Univ Denmark DTU, Cellular Signal Integrat Grp C SIG, Ctr Biol Sequence Anal CBS, Dept Syst Biol, DK-2800 Lyngby, Denmark.
   Inst Syst Biol, Cellular \& Mol Log Unit, Seattle, WA 98103 USA.
   Univ Michigan, Ctr Computat Med \& Bioinformat, Ann Arbor, MI 48109 USA.
   Univ Georgia, Complex Carbohydrate Res Ctr, Athens, GA 30602 USA.
   Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD 21231 USA.
   Univ Calif Los Angeles, David Geffen Sch Med, Los Angeles, CA 90095 USA.
   NCI, Small Business Dev Ctr, NIH, Bethesda, MD 20892 USA.
   La Trobe Univ, La Trobe Inst Mol Sci, Bundoora, Vic 3086, Australia.
   NIH, Natl Ctr Biotechnol Informat, Bethesda, MD 20892 USA.
   Pacific NW Natl Lab, Richland, WA 99352 USA.
   NIST, Chem Reference Data Grp, Gaithersburg, MD 20899 USA.
   Vanderbilt Ingram Canc Ctr, Nashville, TN 37232 USA.
   Natl Inst Neurol Disorders \& Stroke, NIH, Bethesda, MD 20892 USA.
   Scripps Res Inst, La Jolla, CA 92037 USA.},
DOI = {10.1021/pr201071t},
ISSN = {1535-3893},
EISSN = {1535-3907},
Keywords = {selected reaction monitoring; bioinformatics; data quality; metrics;
   open access; Amsterdam Principles; standards},
Keywords-Plus = {PROTEIN IDENTIFICATION DATA; PEPTIDE IDENTIFICATION; CLINICAL
   PROTEOMICS; MINIMUM INFORMATION; STATISTICAL-MODEL; GUIDELINES;
   RESOURCE; REPRODUCIBILITY; PERFORMANCE; VALIDATION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods},
Author-Email = {kinsingc@mail.nih.gov},
Affiliations = {National Institutes of Health (NIH) - USA; NIH National Cancer Institute
   (NCI); Agilent Technologies; Macquarie University; National Institutes
   of Health (NIH) - USA; NIH National Cancer Institute (NCI); University
   of Victoria; University of California System; University of California
   San Francisco; Institute for Systems Biology (ISB); Johns Hopkins
   University; Institute for Systems Biology (ISB); Luxembourg Institute of
   Health; QIMR Berghofer Medical Research Institute; Agilent Technologies;
   Northeastern University; European Molecular Biology Laboratory (EMBL);
   Thermo Fisher Scientific; Roche Holding; Technical University of
   Denmark; Institute for Systems Biology (ISB); University of Michigan
   System; University of Michigan; University System of Georgia; University
   of Georgia; Johns Hopkins University; University of California System;
   University of California Los Angeles; University of California Los
   Angeles Medical Center; David Geffen School of Medicine at UCLA;
   National Institutes of Health (NIH) - USA; NIH National Cancer Institute
   (NCI); La Trobe University; National Institutes of Health (NIH) - USA;
   United States Department of Energy (DOE); Pacific Northwest National
   Laboratory; National Institute of Standards \& Technology (NIST) - USA;
   Vanderbilt University; National Institutes of Health (NIH) - USA; NIH
   National Institute of Neurological Disorders \& Stroke (NINDS); Scripps
   Research Institute},
ResearcherID-Numbers = {Smith, Richard D/J-3664-2012
   Smith, Richard/HMD-4857-2023
   Simpson, Richard/A-6947-2012
   Hermjakob, Henning/AFM-3497-2022
   Moritz, Robert L/B-9222-2011
   Pandey, Akhilesh/B-4127-2009
   Deutsch, Eric/AAF-5912-2020
   BORCHERS, Christoph/U-5964-2019
   },
ORCID-Numbers = {Smith, Richard D/0000-0002-2381-2349
   Hermjakob, Henning/0000-0001-8479-0262
   Pandey, Akhilesh/0000-0001-9943-6127
   Simpson, Richard/0000-0002-9834-0796
   Deutsch, Eric/0000-0001-8732-0928
   Ping, Peipei/0000-0003-3583-3881
   Linding, Rune/0000-0003-0420-4839
   Tabb, David/0000-0001-7223-578X
   Baker, Mark/0000-0001-5858-4035
   Omenn, Gilbert S./0000-0002-8976-6074},
Funding-Acknowledgement = {Intramural NIH HHS {[}Z99 CA999999] Funding Source: Medline; NHGRI NIH
   HHS {[}RC2 HG005805] Funding Source: Medline; NIGMS NIH HHS {[}P50
   GM076547] Funding Source: Medline},
Number-of-Cited-References = {51},
Times-Cited = {14},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {49},
Journal-ISO = {J. Proteome Res.},
Doc-Delivery-Number = {894WN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000300458300077},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000298334000002,
Author = {Kinsinger, Christopher R. and Apffel, James and Baker, Mark and Bian,
   Xiaopeng and Borchers, Christoph H. and Bradshaw, Ralph and Brusniak,
   Mi-Youn and Chan, Daniel W. and Deutsch, Eric W. and Domon, Bruno and
   Gorman, Jeff and Grimm, Rudolf and Hancock, William and Hermjakob,
   Henning and Horn, David and Hunter, Christie and Kolar, Patrik and
   Kraus, Hans-Joachim and Langen, Hanno and Linding, Rune and Moritz,
   Robert L. and Omenn, Gilbert S. and Orlando, Ron and Pandey, Akhilesh
   and Ping, Peipei and Rahbar, Amir and Rivers, Robert and Seymour, Sean
   L. and Simpson, Richard J. and Slotta, Douglas and Smith, Richard D. and
   Stein, Stephen E. and Tabb, David L. and Tagle, Danilo and Yates, III,
   John R. and Rodriguez, Henry},
Title = {Recommendations for mass spectrometry data quality metrics for open
   access data (corollary to the Amsterdam principles)},
Journal = {PROTEOMICS CLINICAL APPLICATIONS},
Year = {2011},
Volume = {5},
Number = {11-12},
Pages = {580-589},
Month = {DEC},
Abstract = {Policies supporting the rapid and open sharing of proteomic data are
   being implemented by the leading journals in the field. The proteomics
   community is taking steps to ensure that data are made publicly
   accessible and are of high quality, a challenging task that requires the
   development and deployment of methods for measuring and documenting data
   quality metrics. On September 18, 2010, the U.S. National Cancer
   Institute (NCI) convened the ``International Workshop on Proteomic Data
   Quality Metrics{''} in Sydney, Australia, to identify and address issues
   facing the development and use of such methods for open access
   proteomics data. The stakeholders at the workshop enumerated the key
   principles underlying a framework for data quality assessment in mass
   spectrometry data that will meet the needs of the research community,
   journals, finding agencies, and data repositories. Attendees discussed
   and agreed up on two primary needs for the wide use of quality metrics:
   (i) an evolving list of comprehensive quality metrics and (ii) standards
   accompanied by software analytics. Attendees stressed the importance of
   increased education and training programs to promote reliable protocols
   in proteomics. This workshop report explores the historic precedents,
   key discussions, and necessary next steps to enhance the quality of open
   access data. By agreement, this article is published simultaneously in
   Proteomics, Proteomics Clinical Applications, Journal of Proteome
   Research, and Molecular and Cellular Proteomics, as a public service to
   the research community. The peer review process was a coordinated effort
   conducted by a panel of referees selected by the journals.},
Publisher = {WILEY-V C H VERLAG GMBH},
Address = {POSTFACH 101161, 69451 WEINHEIM, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Kinsinger, CR (Corresponding Author), NCI, Off Canc Clin Prote Res, NIH, 31 Ctr Dr,MSC 2580, Bethesda, MD 20892 USA.
   Kinsinger, Christopher R.; Rahbar, Amir; Rodriguez, Henry, NCI, Off Canc Clin Prote Res, NIH, Bethesda, MD 20892 USA.
   Apffel, James, Agilent Res Labs, Santa Clara, CA USA.
   Baker, Mark, Macquarie Univ, Dept Chem \& Biomol Sci, Sydney, NSW 2109, Australia.
   Bian, Xiaopeng, NCI, Ctr Bioinformat \& Informat Technol, NIH, Bethesda, MD 20892 USA.
   Borchers, Christoph H., Univ Victoria, Genome BC Prote Ctr, Victoria, BC, Canada.
   Bradshaw, Ralph, Univ Calif San Francisco, Mass Spectrometry Facil, San Francisco, CA 94143 USA.
   Moritz, Robert L., Inst Syst Biol, Cellular \& Mol Log Unit, Seattle, WA USA.
   Chan, Daniel W., Johns Hopkins Univ, Sch Med, Dept Pathol, Baltimore, MD 21205 USA.
   Domon, Bruno, CRP Sante, Luxembourg Clin Prote Ctr, Luxembourg, Luxembourg.
   Gorman, Jeff, Queensland Inst Med Res, Prot Discovery Ctr, Herston, Qld 4006, Australia.
   Grimm, Rudolf, Agilent Technol, Santa Clara, CA USA.
   Hancock, William, Northeastern Univ, Dept Chem \& Chem Biol, Boston, MA 02115 USA.
   Hermjakob, Henning, European Bioinformat Inst, Prote Serv, Cambridge, England.
   Horn, David, Thermo Fisher Sci, Prote Software Strateg Mkt, San Jose, CA USA.
   Hunter, Christie; Rivers, Robert, AB SCIEX, Foster City, CA USA.
   Kolar, Patrik, European Commiss, Directorate Gen Res, Brussels, Belgium.
   Kraus, Hans-Joachim, Wiley VCH, Weinheim, Germany.
   Langen, Hanno, Hoffmann La Roche AG, Exploratory Biomarkers, Basel, Switzerland.
   Linding, Rune, Tech Univ Denmark, C SIG, Ctr Biol Sequence Anal CBS, Dept Syst Biol, DK-2800 Lyngby, Denmark.
   Omenn, Gilbert S., Univ Michigan, Ctr Computat Med \& Bioinformat, Ann Arbor, MI 48109 USA.
   Orlando, Ron, Univ Georgia, Complex Carbohydrate Res Ctr, Athens, GA 30602 USA.
   Pandey, Akhilesh, Johns Hopkins Univ, McKusick Nathans Inst Genet Med, Baltimore, MD USA.
   Ping, Peipei, Univ Calif Los Angeles, David Geffen Sch Med, Los Angeles, CA 90095 USA.
   Seymour, Sean L., NCI, Small Business Dev Ctr, NIH, Bethesda, MD 20892 USA.
   Simpson, Richard J., La Trobe Univ, La Trobe Inst Mol Sci, Bundoora, Vic, Australia.
   Slotta, Douglas, NIH, Ctr Biotechnol Informat, Bethesda, MD 20892 USA.
   Smith, Richard D., Pacific NW Natl Lab, Richland, WA 99352 USA.
   Stein, Stephen E., NIST, Chem Reference Data Grp, Gaithersburg, MD 20899 USA.
   Tabb, David L., Vanderbilt Ingram Canc Ctr, Nashville, TN USA.
   Tagle, Danilo, Natl Inst Neurol Disorders \& Stroke, NIH, Bethesda, MD USA.
   Yates, John R., III, Scripps Res Inst, La Jolla, CA 92037 USA.},
DOI = {10.1002/prca.201100097},
ISSN = {1862-8346},
EISSN = {1862-8354},
Keywords = {Amsterdam principles; Bioinformatics; Data quality; Metrics; Open
   access; Selected reaction monitoring; Standards},
Keywords-Plus = {PROTEIN IDENTIFICATION DATA; PEPTIDE IDENTIFICATION; CLINICAL
   PROTEOMICS; MINIMUM INFORMATION; STATISTICAL-MODEL; GUIDELINES;
   RESOURCE; REPRODUCIBILITY; PERFORMANCE; VALIDATION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
Author-Email = {kinsingc@mail.nih.gov},
Affiliations = {National Institutes of Health (NIH) - USA; NIH National Cancer Institute
   (NCI); Agilent Technologies; Macquarie University; National Institutes
   of Health (NIH) - USA; NIH National Cancer Institute (NCI); University
   of Victoria; University of California System; University of California
   San Francisco; Institute for Systems Biology (ISB); Johns Hopkins
   University; Luxembourg Institute of Health; QIMR Berghofer Medical
   Research Institute; Agilent Technologies; Northeastern University;
   European Molecular Biology Laboratory (EMBL); Thermo Fisher Scientific;
   Roche Holding; Technical University of Denmark; University of Michigan
   System; University of Michigan; University System of Georgia; University
   of Georgia; Johns Hopkins University; University of California System;
   University of California Los Angeles; University of California Los
   Angeles Medical Center; David Geffen School of Medicine at UCLA;
   National Institutes of Health (NIH) - USA; NIH National Cancer Institute
   (NCI); La Trobe University; National Institutes of Health (NIH) - USA;
   United States Department of Energy (DOE); Pacific Northwest National
   Laboratory; National Institute of Standards \& Technology (NIST) - USA;
   Vanderbilt University; National Institutes of Health (NIH) - USA; NIH
   National Institute of Neurological Disorders \& Stroke (NINDS); Scripps
   Research Institute},
ResearcherID-Numbers = {Deutsch, Eric/AAF-5912-2020
   Smith, Richard D/J-3664-2012
   Pandey, Akhilesh/B-4127-2009
   BORCHERS, Christoph/U-5964-2019
   Bradshaw, Ralph A/K-1515-2013
   Smith, Richard/HMD-4857-2023
   Hermjakob, Henning/AFM-3497-2022
   Moritz, Robert L/B-9222-2011
   Simpson, Richard/A-6947-2012
   },
ORCID-Numbers = {Smith, Richard D/0000-0002-2381-2349
   Pandey, Akhilesh/0000-0001-9943-6127
   Hermjakob, Henning/0000-0001-8479-0262
   Omenn, Gilbert S./0000-0002-8976-6074
   Simpson, Richard/0000-0002-9834-0796
   Tabb, David/0000-0001-7223-578X
   Ping, Peipei/0000-0003-3583-3881
   Baker, Mark/0000-0001-5858-4035
   Deutsch, Eric/0000-0001-8732-0928},
Number-of-Cited-References = {51},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {27},
Journal-ISO = {Proteom. Clin. Appl.},
Doc-Delivery-Number = {865TU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000298334000002},
OA = {Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000458552100006,
Author = {Barber, Kathryn and MacLellan, Duncan},
Title = {Examining Open Data at the Urban Level: An Exploration of ``Wellbeing
   Toronto{''}},
Journal = {JOURNAL OF URBAN TECHNOLOGY},
Year = {2019},
Volume = {26},
Number = {1},
Pages = {107-121},
Month = {JAN 2},
Abstract = {This paper examines how Wellbeing Toronto (WT)-a free, open data, GIS
   tool that allows users to map information-has evolved into an extensive
   data repository with robust data analysis capabilities. Explored is the
   progress of open data scholarship in relation to municipal government
   and civic participation. Based on this, the authors note the following:
   (1) as open data becomes increasingly prevalent, a more varied
   understanding of the organization and structure of municipal government
   may emerge. (2) There is a need for measures of civic engagement to move
   beyond data co-production towards an organization-based interactive
   approach.},
Publisher = {ROUTLEDGE JOURNALS, TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Barber, K (Corresponding Author), York Univ, Dept Sociol, Toronto, ON, Canada.
   Barber, Kathryn, York Univ, Dept Sociol, Toronto, ON, Canada.
   MacLellan, Duncan, Ryerson Univ, Dept Polit \& Publ Adm, Toronto, ON, Canada.
   MacLellan, Duncan, Ryerson Univ, Yeates Sch Grad Studies, Toronto, ON, Canada.},
DOI = {10.1080/10630732.2018.1558573},
ISSN = {1063-0732},
EISSN = {1466-1853},
Keywords = {Open data; Toronto; wellbeing; non-profit organizations; civic
   engagement; municipal GIS systems},
Keywords-Plus = {OPEN GOVERNMENT DATA; TRANSPARENCY; TECHNOLOGY; ENGAGEMENT; POLICY},
Research-Areas = {Urban Studies},
Web-of-Science-Categories  = {Urban Studies},
Author-Email = {barberk@yorku.ca},
Affiliations = {York University - Canada; Toronto Metropolitan University},
Funding-Acknowledgement = {Social Science and Humanities Research Council (SSHRC) of Canada
   {[}555310]},
Funding-Text = {This study has been supported financially by the Social Science and
   Humanities Research Council (SSHRC) of Canada (Grant Number 555310).},
Number-of-Cited-References = {27},
Times-Cited = {6},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {20},
Journal-ISO = {J. Urban Technol.},
Doc-Delivery-Number = {HL2QZ},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000458552100006},
DA = {2024-01-15},
}

@article{ WOS:000508205900011,
Author = {Royo-Montanes, Sonia and Benitez-Gomez, Alberto},
Title = {Open data portals. Methodology of analysis and application to Spanish
   municipalities},
Journal = {PROFESIONAL DE LA INFORMACION},
Year = {2019},
Volume = {28},
Number = {6},
Month = {NOV-DEC},
Abstract = {Public administrations publish open data for later reuse by citizens.
   Besides the obvious impact on transparency, they have an important
   economic potential which explains the increasing adoption of this type
   of initiatives. There is an increasing number of administrations that
   decide to create open data portals, a tendency that municipalities have
   followed. Few empirical papers have assessed this type of portals and
   the analyses have been mainly qualitative or limited to a reduced number
   of portals, so there are no generally accepted criteria for the
   assessment of their implementation. The main contribution of this paper
   is the definition of a method to analyse open data portals and its
   application to a sample of municipalities of Spain, a country at the
   forefront of data re-utilization in Europe. Furthermore, the
   economic-financial information available in these portals is analysed,
   as it is essential to accountability, fight corruption and evaluate the
   financial sustainability and effectiveness of public service delivery.
   Results show that there is much room for improvement in this field. Only
   40\% of the cities analysed have an open data portal, and the average
   score of the sample analysed does not reach 50\%. Most portals seem to
   work as mere data repositories, neglecting those aspects that promote
   data use by the non-expert public, accountability, citizen engagement
   and the quality of the data being disclosed (e.g., definition of the
   metadata used). So, the paper concludes with some recommendations for
   improvement.},
Publisher = { EDICIONES PROFESIONALES INFORMACION SL-EPI},
Address = {MISTRAL, 36, BARCELONA, ALBOLOTE, SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {Royo-Montañés, S (Corresponding Author), Univ Zaragoza, Dept Contabilidad \& Finanzas, Fac Econ \& Empresa, Gran Via 2, Zaragoza 50005, Spain.
   Royo-Montanes, Sonia; Benitez-Gomez, Alberto, Univ Zaragoza, Dept Contabilidad \& Finanzas, Fac Econ \& Empresa, Gran Via 2, Zaragoza 50005, Spain.},
DOI = {10.3145/epi.2019.nov.09},
Article-Number = {UNSP e280609},
ISSN = {1386-6710},
Keywords = {Open data; Open data portals; Open government; Transparency;
   Participation; Collaboration; Re-use of public sector information;
   Public sector management; Municipalities; Spain},
Keywords-Plus = {TRANSPARENCY; INFORMATION; QUALITY; REUSE},
Research-Areas = {Communication; Information Science \& Library Science},
Web-of-Science-Categories  = {Communication; Information Science \& Library Science},
Author-Email = {sroyo@unizar.es
   albertobengom@gmail.com},
Affiliations = {University of Zaragoza},
ResearcherID-Numbers = {Royo, Sonia/K-5916-2014},
ORCID-Numbers = {Royo, Sonia/0000-0001-5162-1446},
Number-of-Cited-References = {38},
Times-Cited = {8},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {37},
Journal-ISO = {Prof. Inf.},
Doc-Delivery-Number = {KD9UE},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000508205900011},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000390987000003,
Author = {Taylor, Jason R. and Williams, Nitin and Cusack, Rhodri and Auer, Tibor
   and Shafto, Meredith A. and Dixon, Marie and Tyler, Lorraine K. and
   Cam-Can and Henson, Richard N.},
Title = {The Cambridge Centre for Ageing and Neuroscience (Cam-CAN) data
   repository: Structural and functional MRI, MEG, and cognitive data from
   a cross-sectional adult lifespan sample},
Journal = {NEUROIMAGE},
Year = {2017},
Volume = {144},
Number = {B, SI},
Pages = {262-269},
Month = {JAN 1},
Abstract = {This paper describes the data repository for the Cambridge Centre for
   Ageing and Neuroscience (Cam-CAN) initial study cohort. The Cam-CAN
   Stage 2 repository contains multi-modal (MRI, MEG, and
   cognitive-behavioural) data from a large (approximately N = 700),
   cross-sectional adult lifespan (18-87 years old) population-based
   sample. The study is designed to characterise age-related changes in
   cognition and brain structure and function, and to uncover the
   neurocognitive mechanisms that support healthy cognitive ageing. The
   database contains raw and preprocessed structural MRI, functional MRI
   (active tasks and resting state), and MEG data (active tasks and resting
   state), as well as derived scores from cognitive behavioural experiments
   spanning five broad domains (attention, emotion, action, language, and
   memory), and demographic and neuropsychological data. The dataset thus
   provides a depth of neurocognitive phenotyping that is currently
   unparalleled, enabling integrative analyses of age-related changes in
   brain structure, brain function, and cognition, and providing a testbed
   for novel analyses of multi-modal neuroimaging data. (C) 2015 The
   Authors. Published by Elsevier Inc. This is an open access article under
   the CC BY license.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Taylor, JR (Corresponding Author), Univ Manchester, Sch Psychol Sci, Zochonis Bldg,Brunswick St, Manchester M13 9PL, Lancs, England.
   Taylor, Jason R., Univ Manchester, Sch Psychol Sci, Zochonis Bldg,Brunswick St, Manchester M13 9PL, Lancs, England.
   Williams, Nitin; Auer, Tibor; Henson, Richard N., MRC Cognit \& Brain Sci Unit, 15 Chaucer Rd, Cambridge CB2 7EF, England.
   Cusack, Rhodri, Univ Western Ontario, Brain \& Mind Inst, London, ON, Canada.
   Shafto, Meredith A.; Dixon, Marie; Tyler, Lorraine K., Univ Cambridge, Dept Psychol, Cambridge CB2 3EB, England.
   Cam-Can, Univ Cambridge, Cambridge Ctr Ageing \& Neurosci Cam CAN, Cambridge, England.
   Cam-Can, MRC Cognit \& Brain Sci Unit, Cambridge, England.},
DOI = {10.1016/j.neuroimage.2015.09.018},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords = {Data repository; Brain imaging; Magnetic resonance imaging;
   Magnetoencephalography; Cognition; Ageing},
Keywords-Plus = {EMOTION RECOGNITION; MEMORY; FMRI; INTELLIGENCE; SYSTEM; CORTEX; DAMAGE;
   STATE; TIME},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {jason.taylor@manchester.ac.uk
   nitin.williams@mrc-cbu.cam.ac.uk
   rhodri@cusacklab.org
   tibor.auer@mrc-cbu.cam.ac.uk
   mshafto@csl.psychol.cam.ac.uk
   admin@cam-can.com
   lktyler@csl.psychol.cam.ac.uk
   rik.henson@mrc-cbu.cam.ac.uk},
Affiliations = {University of Manchester; Western University (University of Western
   Ontario); University of Cambridge; University of Cambridge},
ResearcherID-Numbers = {Auer, Tibor/AGF-6766-2022
   Dalgleish, Tim/E-8341-2010
   Williams, Nitin/AAM-5409-2021
   Henson, Richard/H-8822-2019
   Cusack, Rhodri/A-2231-2010
   Rowe, James/C-3661-2013},
ORCID-Numbers = {Dalgleish, Tim/0000-0002-7304-2231
   Henson, Richard/0000-0002-0712-2639
   Mustafa, Abdur/0000-0003-0506-3118
   Auer, Tibor/0000-0001-5153-1424
   Cusack, Rhodri/0000-0002-5234-7415
   Tyler, Lorraine/0000-0002-9943-118X
   Rowe, James/0000-0001-7216-8679},
Funding-Acknowledgement = {Biotechnology and Biological Sciences Research Council {[}BB/H008217/1];
   BBSRC {[}BB/H008217/1] Funding Source: UKRI; MRC {[}MC\_U105579212,
   MC\_U105597119, MC\_UU\_00005/12, MC\_U105579215, MC\_U105579226]
   Funding Source: UKRI; Biotechnology and Biological Sciences Research
   Council {[}BB/H008217/1] Funding Source: researchfish; Medical Research
   Council {[}MC\_U105579226, MC\_U105579212, MC\_U105579215,
   MC\_UU\_00005/12, MC\_U105597119] Funding Source: researchfish; Wellcome
   Trust {[}103838/Z/14/Z] Funding Source: researchfish},
Funding-Text = {The Cambridge Centre for Ageing and Neuroscience (Cam-CAN) research was
   supported by the Biotechnology and Biological Sciences Research Council
   (grant number BB/H008217/1). We are grateful to the Cam-CAN respondents
   and their primary care teams in Cambridge for their participation in
   this study. We also thank the radiographers and MEG operators at the MRC
   Cognition and Brain Sciences Unit facilities for their assistance in
   collecting data.},
Number-of-Cited-References = {43},
Times-Cited = {298},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {59},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {EG4AY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000390987000003},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000594854700001,
Author = {Mendes, Pedro S. F. and Siradze, Sebastien and Pirro, Laura and Thybaut,
   Joris W.},
Title = {Open Data in Catalysis: From Today's Big Picture to the Future of Small
   Data},
Journal = {CHEMCATCHEM},
Year = {2021},
Volume = {13},
Number = {3},
Pages = {836-850},
Month = {FEB 5},
Abstract = {Open science and data are yet to make a real breakthrough and research
   policies will have a critical role in it. The history and general
   context around open data is hence firstly addressed, including how
   researchers perceive the existing incentives, leading to recommendations
   on how to foster data sharing. Subsequently, the focus is on catalysis,
   with a particular emphasis on benchmarking the data sharing practices
   against other fields and surveying the type of data currently being
   shared. The current infrastructure, including data repositories, and
   standards formats is maped. The striking differences among different
   disciplines are discussed, serving as a basis to propose specific
   actions to promote data sharing in catalysis. Short-term initiatives are
   needed to boost the amount of openly available data, particularly in
   heterogeneous catalysis, but a high degree of standardization in data
   formats will be needed to ensure optimal and automated data mining in
   the long run. Because of its unique, central role in understanding the
   catalytic action, kinetic catalytic data is of particular interest. As
   formats and mining tools are dependant on the type of data, kinetic
   catalytic data is firstly characterized. Guidelines for a standardized
   sharing format are proposed, taking into account the small,
   well-structured nature of this type of data. To maximize the extraction
   of information, the low volume of kinetic catalytic data will be
   compensated by incorporating fundamental knowledge into statistics-based
   tools. Whencoupled with knowledge generation tools, i. e. kinetic
   models, new insights at the active site and mechanism levels will be
   reached in an ever more automated and powerful way.},
Publisher = {WILEY-V C H VERLAG GMBH},
Address = {POSTFACH 101161, 69451 WEINHEIM, GERMANY},
Type = {Review},
Language = {English},
Affiliation = {Mendes, PSF; Thybaut, JW (Corresponding Author), Univ Ghent, Dept Mat Text \& Chem Engn, Lab Chem Technol, Technol Pk 125, B-9052 Ghent, Belgium.
   Mendes, Pedro S. F.; Siradze, Sebastien; Pirro, Laura; Thybaut, Joris W., Univ Ghent, Dept Mat Text \& Chem Engn, Lab Chem Technol, Technol Pk 125, B-9052 Ghent, Belgium.},
DOI = {10.1002/cctc.202001132},
EarlyAccessDate = {DEC 2020},
ISSN = {1867-3880},
EISSN = {1867-3899},
Keywords = {Catalysis; open data; kinetics; heterogeneous catalysis; catalysis
   informatics},
Keywords-Plus = {HYDROISOMERIZATION CATALYSTS; SCIENCE; CHALLENGES; DESIGN; INFORMATICS;
   KNOWLEDGE; PLATFORM; METHANE},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Physical},
Author-Email = {pedro.mendes@ugent.be
   joris.thybaut@ugent.be},
Affiliations = {Ghent University},
ResearcherID-Numbers = {Mendes, Pedro S. F./S-4781-2016
   Thybaut, Joris/AAP-5417-2021},
ORCID-Numbers = {Mendes, Pedro S. F./0000-0002-2768-353X
   },
Funding-Acknowledgement = {Ghent University {[}BOF/PDO/2018/001901]},
Funding-Text = {The authors would like to thank Javier Ibanez and Christophe Bouchy for
   the interesting and fruitful discussions. P. S. F. Mendes acknowledges
   the financial support of the Special Research Fund of Ghent University
   for the post-doctoral assistant research mandate (BOF/PDO/2018/001901).},
Number-of-Cited-References = {71},
Times-Cited = {21},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {24},
Journal-ISO = {ChemCatChem},
Doc-Delivery-Number = {QC5RY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000594854700001},
DA = {2024-01-15},
}

@article{ WOS:000698441700001,
Author = {Brantley, Susan L. and Wen, Tao and Agarwal, Deborah A. and Catalano,
   Jeffrey G. and Schroeder, Paul A. and Lehnert, Kerstin and Varadharajan,
   Charuleka and Pett-Ridge, Julie and Engle, Mark and Castronova, Anthony
   M. and Hooper, Richard P. and Ma, Xiaogang and Jin, Lixin and McHenry,
   Kenton and Aronson, Emma and Shaughnessy, Andrew R. and Derry, Louis A.
   and Richardson, Justin and Bales, Jerad and Pierce, Eric M.},
Title = {The future low-temperature geochemical data-scape as envisioned by the
   U. S. geochemical community},
Journal = {COMPUTERS \& GEOSCIENCES},
Year = {2021},
Volume = {157},
Month = {DEC},
Abstract = {Data sharing benefits the researcher, the scientific community, and the
   public by allowing the impact of data to be generalized beyond one
   project and by making science more transparent. However, many scientific
   communities have not developed protocols or standards for publishing,
   citing, and versioning datasets. One community that lags in data
   management is that of low-temperature geochemistry (LTG). This paper
   resulted from an initiative from 2018 through 2020 to convene LTG and
   data scientists in the U.S. to strategize future management of LTG data.
   Through webinars, a workshop, a preprint, a townhall, and a community
   survey, the group of U.S. scientists discussed the landscape of data
   management for LTG - the data-scape. Currently this data-scape includes
   a ``street bazaar{''} of data repositories. This was deemed appropriate
   in the same way that LTG scientists publish articles in many journals.
   The variety of data repositories and journals reflect that LTG
   scientists target many different scientific questions, produce data with
   extremely different structures and volumes, and utilize copious and
   complex metadata. Nonetheless, the group agreed that publication of LTG
   science must be accompanied by sharing of data in publicly accessible
   repositories, and, for sample-based data, registration of samples with
   globally unique persistent identifiers. LTG scientists should use
   certified data repositories that are either highly structured databases
   designed for specialized types of data, or unstructured generalized data
   systems. Recognizing the need for tools to enable search and
   cross-referencing across the proliferating data repositories, the group
   proposed that the overall data informatics paradigm in LTG should shift
   from ``build data repository, data will come{''} to ``publish data
   online, cybertools will find{''}. Funding agencies could also provide
   portals for LTG scientists to register funded projects and datasets, and
   forge approaches that cross national boundaries. The needed
   transformation of the LTG data culture requires emphasis in student
   education on science and management of data.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Brantley, SL (Corresponding Author), Penn State Univ, Earth \& Environm Syst Inst, University Pk, PA 16802 USA.
   Brantley, SL (Corresponding Author), Penn State Univ, Dept Geosci, University Pk, PA 16802 USA.
   Brantley, Susan L., Penn State Univ, Earth \& Environm Syst Inst, University Pk, PA 16802 USA.
   Wen, Tao, Syracuse Univ, Dept Earth \& Environm Sci, Syracuse, NY USA.
   Agarwal, Deborah A., Lawrence Berkeley Natl Lab, Adv Comp Sci Dept, Berkeley, CA USA.
   Catalano, Jeffrey G., Washington Univ, Dept Earth \& Planetary Sci, St Louis, MO 63130 USA.
   Schroeder, Paul A., Univ Georgia, Dept Geol, Athens, GA 30602 USA.
   Lehnert, Kerstin, Columbia Univ, Lamont Doherty Earth Observ, Palisades, NY USA.
   Varadharajan, Charuleka, Lawrence Berkeley Natl Lab, Earth \& Environm Sci Area, Berkeley, CA USA.
   Pett-Ridge, Julie, Oregon State Univ, Dept Crop \& Soil Sci, Corvallis, OR 97331 USA.
   Engle, Mark; Jin, Lixin, Univ Texas El Paso, Dept Geol Sci, El Paso, TX 79968 USA.
   Castronova, Anthony M.; Bales, Jerad, Consortium Univ Adv Hydrol Sci Inc, Cambridge, MA USA.
   Hooper, Richard P., Tufts Univ, Dept Civil \& Environm Engn, Medford, MA 02155 USA.
   Ma, Xiaogang, Univ Idaho, Dept Comp Sci, Moscow, ID 83843 USA.
   McHenry, Kenton, Univ Illinois, Natl Ctr Supercomp Applicat, Urbana, IL 61801 USA.
   Aronson, Emma, Univ Calif Riverside, Dept Microbiol \& Plant Pathol, Riverside, CA 92521 USA.
   Brantley, Susan L.; Shaughnessy, Andrew R., Penn State Univ, Dept Geosci, University Pk, PA 16802 USA.
   Derry, Louis A., Cornell Univ, Dept Earth \& Atmospher Sci, Ithaca, NY USA.
   Richardson, Justin, Univ Massachusetts, Dept Geosci, Amherst, MA 01003 USA.
   Pierce, Eric M., Oak Ridge Natl Lab, Environm Sci Div, Oak Ridge, TN USA.},
DOI = {10.1016/j.cageo.2021.104933},
EarlyAccessDate = {SEP 2021},
Article-Number = {104933},
ISSN = {0098-3004},
EISSN = {1873-7803},
Keywords = {Data management; Data repositories; Geochemistry; Metadata; Data
   sharing; Open science},
Keywords-Plus = {WATER},
Research-Areas = {Computer Science; Geology},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Geosciences,
   Multidisciplinary},
Author-Email = {sxb7@psu.edu},
Affiliations = {Pennsylvania Commonwealth System of Higher Education (PCSHE);
   Pennsylvania State University; Pennsylvania State University -
   University Park; Syracuse University; United States Department of Energy
   (DOE); Lawrence Berkeley National Laboratory; Washington University
   (WUSTL); University System of Georgia; University of Georgia; Columbia
   University; United States Department of Energy (DOE); Lawrence Berkeley
   National Laboratory; Oregon State University; University of Texas
   System; University of Texas El Paso; Tufts University; Idaho; University
   of Idaho; University of Illinois System; University of Illinois
   Urbana-Champaign; University of California System; University of
   California Riverside; Pennsylvania Commonwealth System of Higher
   Education (PCSHE); Pennsylvania State University; Pennsylvania State
   University - University Park; Cornell University; University of
   Massachusetts System; University of Massachusetts Amherst; United States
   Department of Energy (DOE); Oak Ridge National Laboratory},
ResearcherID-Numbers = {Varadharajan, Charuleka/G-3741-2015
   Ma, Xiaogang (Marshall)/C-9286-2011
   Varadharajan, Charuleka/S-4238-2019
   Aronson, Emma L/I-3277-2012
   Derry, Louis A/H-5637-2016
   Catalano, Jeffrey/A-8322-2013
   Wen, Tao/P-6733-2018
   },
ORCID-Numbers = {Varadharajan, Charuleka/0000-0002-4142-3224
   Ma, Xiaogang (Marshall)/0000-0002-9110-7369
   Varadharajan, Charuleka/0000-0002-4142-3224
   Derry, Louis A/0000-0001-7062-7333
   Catalano, Jeffrey/0000-0001-9311-977X
   Lehnert, Kerstin/0000-0001-7036-1977
   Aronson, Emma/0000-0002-5018-2688
   Castronova, Anthony/0000-0002-1341-5681
   Wen, Tao/0000-0002-6113-7532
   Schroeder, Paul/0000-0003-2557-4644},
Funding-Acknowledgement = {U.S. National Science Foundation {[}EAR 19-39257]; U.S. Department of
   Energy's Office of Science {[}DE-AC02-05CH11231];  {[}EAR-GEO-1331846]},
Funding-Text = {This paper was initiated during a workshop held February 18-20 (2020)
   that was funded by the U.S. National Science Foundation (EAR 19-39257 to
   S. L.. Brantley) . The workshop, where twenty-four in-stitutions were
   represented, was organized by S. L. Brantley, T. Wen, D. Agarwal, and J.
   G. Catalano. All participants engaged in the ideas in the paper but
   some, not listed as coauthors, did not work on this document. Those
   latter participants included E. Barrera, P. Bennett, O. Harvey, R.
   Hazen, N. Kabengi, M. Leon, S. Morrison, C. Reinhard, J. Tang, and K.
   Williams. Some authors could not participate in the workshop. Four
   webinars were run prior to the workshop: D. Agarwal (11/25/2019) ; X. Ma
   (12/16/2019) ; K. Lehnert (1/17/2020) ; J. Bales (1/31/2020) . An
   earlier version of this manuscript was posted at EarthArXiv (https://ear
   tharxiv.org/repository/view/1839/) , and was sent out to 350 LTG
   sci-entists funded in the U.S. with an online survey. Twenty-seven
   scientists responded to the survey and 24 scientists participated in an
   online townhall discussion. Support for P. Schroeder is acknowledged
   from EAR-GEO-1331846. D.Agarwal and C.Varadharajan were funded as part
   of the ESS-DIVE project by the U.S. Department of Energy's Office of
   Science under Contract No. DE-AC02-05CH11231. Helpful reviews from two
   anonymous reviewers and Francis Albarede and associate editor Pierre
   Lanari are acknowledged.},
Number-of-Cited-References = {65},
Times-Cited = {5},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {26},
Journal-ISO = {Comput. Geosci.},
Doc-Delivery-Number = {UT9QF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000698441700001},
OA = {hybrid, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000783859500005,
Author = {Quemy, Alexandre and Wrembel, Robert},
Title = {ECHR-OD: On building an integrated open repository of legal documents
   for machine learning applications},
Journal = {INFORMATION SYSTEMS},
Year = {2022},
Volume = {106},
Month = {MAY},
Abstract = {This paper presents an exhaustive and unified repository of judgments
   documents, called ECHR-OD , based on the European Court of Human Rights.
   The need of such a repository is explained through the prism of the
   researcher, the data scientist, the citizen, and the legal practitioner.
   Contrarily to many open data repositories, the full creation process of
   ECHR-OD , from the collection of raw data to the feature transformation,
   is provided by means of a collection of fully automated and open-source
   scripts. It ensures reproducibility and a high level of confidence in
   the processed data, which is one of the most important issues in data
   governance nowadays. The experimental evaluation was performed to study
   the problem of predicting the outcome of a case, and to establish
   baseline results of popular machine learning algorithms. The obtained
   results are consistently good across the binary datasets with an
   accuracy comprised between 75.86\% and 98.32\%, having the average
   accuracy equals to 96.45\%, which is 14pp higher than the best known
   result with similar methods. We achieved a F1-Score of 82\% which is
   aligned with the recent result using BERT. We show that in a multilabel
   setting, the features available prior to a judgment are good predictors
   of the outcome, opening the road to practical applications. (C) 2021
   Elsevier Ltd. All rights reserved.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Quemy, A (Corresponding Author), IBM Krakow Software Lab, Krakow, Poland.
   Quemy, Alexandre; Wrembel, Robert, IBM Krakow Software Lab, Krakow, Poland.
   Quemy, Alexandre, Poznan Univ Tech, Poznan, Poland.},
DOI = {10.1016/j.is.2021.101822},
EarlyAccessDate = {FEB 2022},
Article-Number = {101822},
ISSN = {0306-4379},
EISSN = {1873-6076},
Keywords = {Open data repository; Legal documents repository; Judgment documents;
   European Court of Human Rights; Machine learning; Classification of
   legal documents},
Keywords-Plus = {CURRENT STATE},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Author-Email = {aquemy@pl.ibm.com
   robert.wrembel@cs.put.poznan.pl},
Affiliations = {Poznan University of Technology},
ResearcherID-Numbers = {Wrembel, Robert/F-7482-2014
   },
ORCID-Numbers = {Wrembel, Robert/0000-0001-6037-5718
   Quemy, Alexandre/0000-0002-5865-6403},
Number-of-Cited-References = {29},
Times-Cited = {1},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Inf. Syst.},
Doc-Delivery-Number = {0O9QY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000783859500005},
DA = {2024-01-15},
}

@article{ WOS:000869929800001,
Author = {Campbell, Rebecca and Goodman-Williams, Rachael and Javorka, McKenzie
   and Engleton, Jasmine and Gregory, Katie},
Title = {Understanding Sexual Assault Survivors' Perspectives on Archiving
   Qualitative Data: Implications for Feminist Approaches to Open Science},
Journal = {PSYCHOLOGY OF WOMEN QUARTERLY},
Year = {2023},
Volume = {47},
Number = {1},
Pages = {51-64},
Month = {MAR},
Abstract = {The open science movement has framed data sharing as necessary and
   achievable best practices for high-quality science. Feminist
   psychologists have complicated that narrative by questioning the purpose
   of data sharing across different paradigms, methodologies, and research
   populations. In these debates, the academic community has centered the
   needs and voices of researchers, and participants' perspectives are
   largely missing from this literature. In this study, we sought to
   understand how research participants feel about sharing qualitative data
   on a sensitive subject-sexual victimization. As part of a participatory
   action research project, we conducted qualitative interviews with sexual
   assault survivors about their post-assault help-seeking experiences. The
   federal funding agency that supported this project requires researchers
   to archive de-identified data in a national data repository (the
   National Archive of Criminal Justice Data {[}NACJD]). All participants
   consented to archiving data, and the vast majority expressed positive
   views about data sharing because they wanted to help other survivors.
   Participants emphasized that our participatory action research approach
   and our stated goal of helping survivors were important considerations
   in their decisions regarding data sharing. Researchers should obtain
   informed consent from their participants for data sharing/archiving, and
   discuss their dissemination plans during the informed consent process.},
Publisher = {SAGE PUBLICATIONS LTD},
Address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Campbell, R (Corresponding Author), Michigan State Univ, Dept Psychol, 127 Psychol Bldg,316 Phys Rd, E Lansing, MI 48824 USA.
   Campbell, Rebecca; Javorka, McKenzie; Engleton, Jasmine; Gregory, Katie, Michigan State Univ, Dept Psychol, 127 Psychol Bldg,316 Phys Rd, E Lansing, MI 48824 USA.
   Goodman-Williams, Rachael, Wichita State Univ, Wichita, KS USA.},
DOI = {10.1177/03616843221131546},
EarlyAccessDate = {OCT 2022},
ISSN = {0361-6843},
EISSN = {1471-6402},
Keywords = {open science; qualitative interviews; data sharing; archiving; sexual
   assault},
Keywords-Plus = {PSYCHOLOGY; INTERVIEWS; BARRIERS},
Research-Areas = {Psychology; Women's Studies},
Web-of-Science-Categories  = {Psychology, Multidisciplinary; Women's Studies},
Author-Email = {rmc@msu.edu},
Affiliations = {Michigan State University; Wichita State University},
ResearcherID-Numbers = {Campbell, Rebecca/A-2631-2019},
ORCID-Numbers = {Campbell, Rebecca/0000-0003-0442-9835},
Funding-Acknowledgement = {U.S. Department of Justice, Office on Violence Against Women
   {[}2018-SI-AX-0001]},
Funding-Text = {The authors disclosed receipt of the following financial support for the
   research, authorship, and/or publication of this article: This research
   was supported by a grant from the U.S. Department of Justice, Office on
   Violence Against Women (2018-SI-AX-0001).},
Number-of-Cited-References = {58},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Psychol. Women Q.},
Doc-Delivery-Number = {I0TF3},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000869929800001},
DA = {2024-01-15},
}

@article{ WOS:000693638800037,
Author = {Fondrie, William E. and Bittremieux, Wout and Noble, William S.},
Title = {ppx: Programmatic Access to Proteomics Data Repositories},
Journal = {JOURNAL OF PROTEOME RESEARCH},
Year = {2021},
Volume = {20},
Number = {9},
Pages = {4621-4624},
Month = {SEP 3},
Abstract = {The volume of proteomics and mass spectrometry data available in public
   repositories continues to grow at a rapid pace as more researchers
   embrace open science practices. Open access to the data behind
   scientific discoveries has become critical to validate published
   findings and develop new computational tools. Here, we present ppx, a
   Python package that provides easy, programmatic access to the data
   stored in ProteomeXchange repositories, such as PRIDE and MassIVE. The
   ppx package can be used as either a command line tool or a Python
   package to retrieve the files and metadata associated with a project
   when provided its identifier. To demonstrate how ppx enhances
   reproducible research, we used ppx within a Snakemake workflow to
   reanalyze a published data set with the open modification search tool
   ANN-SoLo and compared our reanalysis to the original results. We show
   that ppx readily integrates into workflows, and our reanalysis produced
   results consistent with the original analysis. We envision that ppx will
   be a valuable tool for creating reproducible analyses, providing tool
   developers easy access to data for development, testing, and
   benchmarking, and enabling the use of mass spectrometry data in
   data-intensive analyses. The ppx package is freely available and open
   source under the MIT license at https://github.com/wfondrie/ppx.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Noble, WS (Corresponding Author), Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA.
   Noble, WS (Corresponding Author), Univ Washington, Paul G Allen Sch Comp Sci \& Engn, Seattle, WA 98195 USA.
   Fondrie, William E.; Noble, William S., Univ Washington, Dept Genome Sci, Seattle, WA 98195 USA.
   Bittremieux, Wout, Univ Calif San Diego, Skaggs Sch Pharm \& Pharmaceut Sci, La Jolla, CA 92093 USA.
   Bittremieux, Wout, Univ Antwerp, Dept Comp Sci, B-2020 Antwerp, Belgium.
   Noble, William S., Univ Washington, Paul G Allen Sch Comp Sci \& Engn, Seattle, WA 98195 USA.},
DOI = {10.1021/acs.jproteome.1c00454},
EarlyAccessDate = {AUG 2021},
ISSN = {1535-3893},
EISSN = {1535-3907},
Keywords = {proteomics; mass spectrometry; bioinformatics; reproducibility;
   repository; data sharing; data dissemination; data access; Python; FAIR},
Keywords-Plus = {SHOTGUN PROTEOMICS; SPECTRA; DRAFT},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods},
Author-Email = {william-noble@uw.edu},
Affiliations = {University of Washington; University of Washington Seattle; University
   of California System; University of California San Diego; University of
   Antwerp; University of Washington; University of Washington Seattle},
ResearcherID-Numbers = {Fondrie, William E/M-1468-2015
   },
ORCID-Numbers = {Fondrie, William E/0000-0002-1554-3716
   Bittremieux, Wout/0000-0002-3105-1359
   Noble, William/0000-0001-7283-4715},
Funding-Acknowledgement = {National Institutes of Health {[}T32HG000035, P41GM103533, R01GM121818];
   Research Foundation-Flanders {[}FWO 12W0418N]},
Funding-Text = {The research reported in this publication was supported by the National
   Institutes of Health Award Nos. T32HG000035, P41GM103533, and
   R01GM121818. W.B. is a postdoctoral researcher of the Research
   Foundation-Flanders (FWO 12W0418N).},
Number-of-Cited-References = {30},
Times-Cited = {6},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {4},
Journal-ISO = {J. Proteome Res.},
Doc-Delivery-Number = {UM9IW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000693638800037},
OA = {Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000460555700004,
Author = {Sicilia, Miguel-Angel and Visvizi, Anna},
Title = {Blockchain and OECD data repositories: opportunities and policymaking
   implications},
Journal = {LIBRARY HI TECH},
Year = {2019},
Volume = {37},
Number = {1, SI},
Pages = {30-42},
Month = {MAR 18},
Abstract = {Purpose The purpose of this paper is to employ the case of Organization
   for Economic Cooperation and Development (OECD) data repositories to
   examine the potential of blockchain technology in the context of
   addressing basic contemporary societal concerns, such as transparency,
   accountability and trust in the policymaking process. Current approaches
   to sharing data employ standardized metadata, in which the provider of
   the service is assumed to be a trusted party. However, derived data,
   analytic processes or links from policies, are in many cases not shared
   in the same form, thus breaking the provenance trace and making the
   repetition of analysis conducted in the past difficult. Similarly, it
   becomes tricky to test whether certain conditions justifying policies
   implemented still apply. A higher level of reuse would require a
   decentralized approach to sharing both data and analytic scripts and
   software. This could be supported by a combination of blockchain and
   decentralized file system technology. Design/methodology/approach The
   findings presented in this paper have been derived from an analysis of a
   case study, i.e., analytics using data made available by the OECD. The
   set of data the OECD provides is vast and is used broadly. The argument
   is structured as follows. First, current issues and topics shaping the
   debate on blockchain are outlined. Then, a redefinition of the main
   artifacts on which some simple or convoluted analytic results are based
   is revised for some concrete purposes. The requirements on provenance,
   trust and repeatability are discussed with regards to the architecture
   proposed, and a proof of concept using smart contracts is used for
   reasoning on relevant scenarios. Findings A combination of decentralized
   file systems and an open blockchain such as Ethereum supporting smart
   contracts can ascertain that the set of artifacts used for the analytics
   is shared. This enables the sequence underlying the successive stages of
   research and/or policymaking to be preserved. This suggests that, in
   turn, and ex post, it becomes possible to test whether evidence
   supporting certain findings and/or policy decisions still hold.
   Moreover, unlike traditional databases, blockchain technology makes it
   possible that immutable records can be stored. This means that the
   artifacts can be used for further exploitation or repetition of results.
   In practical terms, the use of blockchain technology creates the
   opportunity to enhance the evidence-based approach to policy design and
   policy recommendations that the OECD fosters. That is, it might enable
   the stakeholders not only to use the data available in the OECD
   repositories but also to assess corrections to a given policy strategy
   or modify its scope.
   Research limitations/implications - Blockchains and related technologies
   are still maturing, and several questions related to their use and
   potential remain underexplored. Several issues require particular
   consideration in future research, including anonymity, scalability and
   stability of the data repository. This research took as example OECD
   data repositories, precisely to make the point that more research and
   more dialogue between the research and policymaking community is needed
   to embrace the challenges and opportunities blockchain technology
   generates. Several questions that this research prompts have not been
   addressed. For instance, the question of how the sharing economy concept
   for the specifics of the case could be employed in the context of
   blockchain has not been dealt with.
   Practical implications - The practical implications of the research
   presented here can be summarized in two ways. On the one hand, by
   suggesting how a combination of decentralized file systems and an open
   blockchain, such as Ethereum supporting smart contracts, can ascertain
   that artifacts are shared, this paper paves the way toward a discussion
   on how to make this approach and solution reality. The approach and
   architecture proposed in this paper would provide a way to increase the
   scope of the reuse of statistical data and results and thus would
   improve the effectiveness of decision making as well as the transparency
   of the evidence supporting policy.
   Social implications - Decentralizing analytic artifacts will add to
   existing open data practices an additional layer of benefits for
   different actors, including but not limited to policymakers,
   journalists, analysts and/or researchers without the need to establish
   centrally managed institutions. Moreover, due to the degree of
   decentralization and absence of a single-entry point, the vulnerability
   of data repositories to cyberthreats might be reduced. Simultaneously,
   by ensuring that artifacts derived from data based in those distributed
   depositories are made immutable therein, full reproducibility of
   conclusions concerning the data is possible. In the field of data-driven
   policymaking processes, it might allow policymakers to devise more
   accurate ways of addressing pressing issues and challenges.
   Originality/value - This paper offers the first blueprint of a form of
   sharing that complements open data practices with the decentralized
   approach of blockchain and decentralized file systems. The case of OECD
   data repositories is used to highlight that while data storing is
   important, the real added value of blockchain technology rests in the
   possible change on how we use the data and data sets in the
   repositories. It would eventually enable a more transparent and
   actionable approach to linking policy up with the supporting evidence.
   From a different angle, throughout the paper the case is made that
   rather than simply data, artifacts from conducted analyses should be
   made persistent in a blockchain. What is at stake is the full
   reproducibility of conclusions based on a given set of data, coupled
   with the possibility of ex post testing the validity of the assumptions
   and evidence underlying those conclusions.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Sicilia, MA (Corresponding Author), Univ Alcala, Dept Comp Sci, Alcala De Henares, Spain.
   Sicilia, Miguel-Angel, Univ Alcala, Dept Comp Sci, Alcala De Henares, Spain.
   Visvizi, Anna, Amer Coll Greece, Deree Coll, Sch Business \& Econ, Athens, Greece.
   Visvizi, Anna, Effat Univ, Coll Business, Jeddah, Saudi Arabia.},
DOI = {10.1108/LHT-12-2017-0276},
ISSN = {0737-8831},
Keywords = {OECD; Decentralization; Blockchain; Ethereum; IPFS; Open archives},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {msicilia@uah.es},
Affiliations = {Universidad de Alcala; Effat University},
ResearcherID-Numbers = {Visvizi, Anna/AAF-4156-2019
   Visvizi, Anna/AFV-1944-2022
   },
ORCID-Numbers = {Visvizi, Anna/0000-0003-3240-3771
   Miguel Angel, Sicilia Urban/0000-0003-3067-4180},
Number-of-Cited-References = {43},
Times-Cited = {27},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {83},
Journal-ISO = {Libr. Hi Tech},
Doc-Delivery-Number = {HN9YE},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000460555700004},
DA = {2024-01-15},
}

@article{ WOS:000674301400097,
Author = {Murphy, Fiona and Bar-Sinai, Michael and Martone, Maryann E.},
Title = {A tool for assessing alignment of biomedical data repositories with
   open, FAIR, citation and trustworthy principles},
Journal = {PLOS ONE},
Year = {2021},
Volume = {16},
Number = {7},
Month = {JUL 9},
Abstract = {Increasing attention is being paid to the operation of biomedical data
   repositories in light of efforts to improve how scientific data is
   handled and made available for the long term. Multiple groups have
   produced recommendations for functions that biomedical repositories
   should support, with many using requirements of the FAIR data principles
   as guidelines. However, FAIR is but one set of principles that has
   arisen out of the open science community. They are joined by principles
   governing open science, data citation and trustworthiness, all of which
   are important aspects for biomedical data repositories to support.
   Together, these define a framework for data repositories that we call
   OFCT: Open, FAIR, Citable and Trustworthy. Here we developed an
   instrument using the open source PolicyModels toolkit that attempts to
   operationalize key aspects of OFCT principles and piloted the instrument
   by evaluating eight biomedical community repositories listed by the
   NIDDK Information Network (dkNET.org). Repositories included both
   specialist repositories that focused on a particular data type or
   domain, in this case diabetes and metabolomics, and generalist
   repositories that accept all data types and domains. The goal of this
   work was both to obtain a sense of how much the design of current
   biomedical data repositories align with these principles and to augment
   the dkNET listing with additional information that may be important to
   investigators trying to choose a repository, e.g., does the repository
   fully support data citation? The evaluation was performed from March to
   November 2020 through inspection of documentation and interaction with
   the sites by the authors. Overall, although there was little explicit
   acknowledgement of any of the OFCT principles in our sample, the
   majority of repositories provided at least some support for their
   tenets.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Martone, ME (Corresponding Author), Univ Calif San Diego, Dept Neurosci, SciCrunch Inc, San Diego, CA 92103 USA.
   Murphy, Fiona, MoreBrains Cooperat Ltd, Chichester, England.
   Bar-Sinai, Michael, Ben Gurion Univ Negev, Dept Comp Sci, Beer Sheva, Israel.
   Bar-Sinai, Michael, Harvard Univ, Inst Quantitat Social Sci, Beer Sheva, Israel.
   Martone, Maryann E., Univ Calif San Diego, Dept Neurosci, SciCrunch Inc, San Diego, CA 92103 USA.},
DOI = {10.1371/journal.pone.0253538},
Article-Number = {e0253538},
ISSN = {1932-6203},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {mmartone@ucsd.edu},
Affiliations = {Ben Gurion University; University of California System; University of
   California San Diego},
ORCID-Numbers = {Murphy, Fiona/0000-0003-1693-1240
   Bar-Sinai, Michael/0000-0002-0153-8465
   Martone, Maryann/0000-0002-8406-3871},
Funding-Acknowledgement = {NIH from the National Institutes of Diabetes and Digestive and Kidney
   Diseases {[}3U24DK097771-08S1]; Leona M. and Harry B. Helmsley
   Charitable Trust Biomedical Research Infrastructure Program},
Funding-Text = {This work was supported by NIH grant\#3U24DK097771-08S1 from the
   National Institutes of Diabetes and Digestive and Kidney Diseases. The
   original decision tree was developed through the FORCE11 Scholarly
   Commons working group supported by an award from The Leona M. and Harry
   B. Helmsley Charitable Trust Biomedical Research Infrastructure Program
   to FORCE11. The authors wish to thank Drs. Ko Wei Lin and Jeffrey Grethe
   for helpful comments. Fiona Murphy is employed by MoreBrains Cooperative
   Ltd, Chichester, UK, a commercial company that did not provide any
   direct funding for this project and does not have any direct interests
   in the repositories, dkNET or NIH. The funder provided support to UCSD
   for this work which was paid in the form of salaries for MM and
   subcontracts to FM and MBS, but did not have any additional role in the
   study design, data collection and analysis, decision to publish, or
   preparation of the manuscript. The specific roles of these authors are
   articulated in the `author contributions `section.},
Number-of-Cited-References = {27},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {9},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {TK6YI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000674301400097},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000743496700060,
Author = {Shi, Guobang and Kang, Xinyue and Dong, Fanyi and Liu, Yanchao and Zhu,
   Ning and Hu, Yuxuan and Xu, Hanmei and Lao, Xingzhen and Zheng, Heng},
Title = {DRAMP 3.0: an enhanced comprehensive data repository of antimicrobial
   peptides},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2022},
Volume = {50},
Number = {D1},
Pages = {D488-D496},
Month = {JAN 7},
Abstract = {Stapled antimicrobial peptides are an emerging class of artificial
   cyclic peptide molecules which have antimicrobial activity and potent
   structure stability. We previously published the Data Repository of
   Antimicrobial Peptides (DRAMP) as a manually annotated and open-access
   database of antimicrobial peptides (AMPs). In the update of version 3.0,
   special emphasis was placed on the new development of stapled AMPs, and
   a subclass of specific AMPs was added to store information on these
   special chemically modified AMPs. To help design low toxicity AMPs, we
   also added the cytotoxicity property of AMPs, as well as the expansion
   of newly discovered AMP data. At present, DRAMP has been expanded and
   contains 22259 entries (2360 newly added), consisting of 5891 general
   entries, 16110 patent entries, 77 clinical entries and 181 stapled AMPs.
   A total of 263 entries have predicted structures, and more than 300
   general entries have links to experimentally determined structures in
   the Protein Data Bank. The update also covers new annotations,
   statistics, categories, functions and download links. DRAMP is available
   online at http://dramp.cpu-bioinfor.org/.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Lao, XZ; Zheng, H (Corresponding Author), China Pharmaceut Univ, Sch Life Sci \& Technol, Nanjing 211100, Peoples R China.
   Shi, Guobang; Kang, Xinyue; Dong, Fanyi; Liu, Yanchao; Zhu, Ning; Lao, Xingzhen; Zheng, Heng, China Pharmaceut Univ, Sch Life Sci \& Technol, Nanjing 211100, Peoples R China.
   Hu, Yuxuan, China Pharmaceut Univ, Sch Int Pharmaceut Business, Nanjing 211100, Peoples R China.
   Xu, Hanmei, China Pharmaceut Univ, Engn Res Ctr Peptide Drug Discovery \& Dev, Nanjing 211100, Peoples R China.},
DOI = {10.1093/nar/gkab651},
EarlyAccessDate = {AUG 2021},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENERATION; BIOLOGY; TOOLS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {lao@cpu.edu.cn
   zhengh18@hotmail.com},
Affiliations = {China Pharmaceutical University; China Pharmaceutical University; China
   Pharmaceutical University},
ResearcherID-Numbers = {Hu, Yuxuan/JNE-9368-2023
   },
ORCID-Numbers = {Hu, Yuxuan/0000-0003-2931-2991
   Shi, Guobang/0000-0003-2480-9720},
Funding-Acknowledgement = {National Natural Science Foundation of China {[}82073767]; Priority
   Academic Program Development of Jiangsu Higher Education Institutions
   {[}PAPD201465]},
Funding-Text = {National Natural Science Foundation of China {[}82073767]; Priority
   Academic Program Development of Jiangsu Higher Education Institutions
   {[}PAPD2014-65]; Fundig for open access charge: National Natural Science
   Foundation of China {[}82073767]; Priority Academic Program Development
   of Jiangsu Higher Education Institutions {[}PAPD201465].},
Number-of-Cited-References = {48},
Times-Cited = {73},
Usage-Count-Last-180-days = {9},
Usage-Count-Since-2013 = {30},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {YH9RO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000743496700060},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000452544100067,
Author = {Miller, Renee J.},
Title = {Open Data Integration},
Journal = {PROCEEDINGS OF THE VLDB ENDOWMENT},
Year = {2018},
Volume = {11},
Number = {12},
Pages = {2130-2139},
Month = {AUG},
Abstract = {Open data plays a major role in supporting both governmental and
   organizational transparency. Many organizations are adopting Open Data
   Principles promising to make their open data complete, primary, and
   timely. These properties make this data tremendously valuable to data
   scientists. However, scientists generally do not have a priori knowledge
   about what data is available (its schema or content). Nevertheless, they
   want to be able to use open data and integrate it with other public or
   private data they are studying. Traditionally, data integration is done
   using a framework called query discovery where the main task is to
   discover a query (or transformation) that translates data from one form
   into another. The goal is to find the right operators to join, nest,
   group, link, and twist data into a desired form. We introduce a new
   paradigm for thinking about integration where the focus is on data
   discovery, but highly efficient internet-scale discovery that is driven
   by data analysis needs. We describe a research agenda and recent
   progress in developing scalable data-analysis or query-aware data
   discovery algorithms that provide high recall and accuracy over massive
   data repositories.},
Publisher = {ASSOC COMPUTING MACHINERY},
Address = {2 PENN PLAZA, STE 701, NEW YORK, NY 10121-0701 USA},
Type = {Article},
Language = {English},
Affiliation = {Miller, RJ (Corresponding Author), Northeastern Univ, Boston, MA 02115 USA.
   Miller, Renee J., Northeastern Univ, Boston, MA 02115 USA.},
DOI = {10.14778/3229863.3240491},
ISSN = {2150-8097},
Keywords-Plus = {DATA EXCHANGE; SCHEMA; TABLES; ALGORITHMS; QUERIES; SEARCH},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Computer Science, Theory \&
   Methods},
Author-Email = {miller@northeastern.edu},
Affiliations = {Northeastern University},
Funding-Acknowledgement = {NSERC; Northeastern College of Computer and Information Science},
Funding-Text = {I would like to give a special thank you to Fatemeh Nargesian and Ken Q.
   Pu for their help and insights on this paper, and to Erkang Zhu for his
   help and the statistics. Many of these ideas were also influenced by
   collaborations with: Periklis Andritsos, Bahar Ghadiri Bashardoost,
   Christina Christodoulakis, and Carolina Simoes Gomes. I would also like
   to thank Laura Haas, Lucian Popa, and Wang-Chiew Tan for very helpful
   comments on a draft of this paper. A final thank you to Dong Deng for
   providing statistics on the MIT warehouse. NSERC funded this work along
   with the Northeastern College of Computer and Information Science.},
Number-of-Cited-References = {78},
Times-Cited = {42},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Proc. VLDB Endow.},
Doc-Delivery-Number = {HD5CA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000452544100067},
DA = {2024-01-15},
}

@article{ WOS:000533012500001,
Author = {Dogan, Guleda and Taskin, Zehra and Aydinoglu, Arsev Umur},
Title = {Research data management in Turkey: A survey to build an effective
   national data repository},
Journal = {IFLA JOURNAL-INTERNATIONAL FEDERATION OF LIBRARY ASSOCIATIONS},
Year = {2021},
Volume = {47},
Number = {1},
Pages = {51-64},
Month = {MAR},
Abstract = {Research data management is an important topic for funding agencies,
   universities and researchers. In this context, the main aim of this
   study is to collect preliminary information for Aperta, which is being
   developed by the Scientific and Technological Research Council of
   Turkey, to fulfil the following goals: determine the research data
   management awareness levels of researchers in Turkey; understand current
   research data management practices in their research environments; and
   find out their experiences of policy issues. For this, a questionnaire
   was distributed to 37,223 researchers, with 1577 researchers completing
   it. The results indicated that researchers who spend more time with data
   have more concerns about data management issues. The levels of
   experience of creating a data management plan were quite low. The
   importance of this study lies in how it is able to show the current
   research data management practices of Turkish scholars during the new
   repository's foundational development stage.},
Publisher = {SAGE PUBLICATIONS INC},
Address = {2455 TELLER RD, THOUSAND OAKS, CA 91320 USA},
Type = {Article},
Language = {English},
Affiliation = {Taskin, Z (Corresponding Author), Adam Mickiewicz Univ, Miedzychodzka 5, PL-60371 Poznan, Poland.
   Dogan, Guleda; Taskin, Zehra, Hacettepe Univ, Dept Informat Manegement, Ankara, Turkey.
   Taskin, Zehra, Adam Mickiewicz Univ, Scholarly Commun Res Grp, Poznan, Poland.
   Aydinoglu, Arsev Umur, Middle East Tech Univ, Sci \& Technol Policy Studies, Ankara, Turkey.},
DOI = {10.1177/0340035220917985},
EarlyAccessDate = {APR 2020},
Article-Number = {0340035220917985},
ISSN = {0340-0352},
EISSN = {1745-2651},
Keywords = {Data services; services to user populations; research data management;
   data repository; Turkey; data practices; open data},
Keywords-Plus = {BIG DATA; INCENTIVES; PREVALENCE; TRUTH; NEED},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {zehrayanar@gmail.com},
Affiliations = {Hacettepe University; Adam Mickiewicz University; Middle East Technical
   University},
ResearcherID-Numbers = {DOGAN, GULEDA/I-8996-2013
   Taskin, Zehra/H-3025-2011
   Aydinoglu, Arsev Umur/A-5455-2016},
ORCID-Numbers = {DOGAN, GULEDA/0000-0001-7435-3181
   Taskin, Zehra/0000-0001-7102-493X
   Aydinoglu, Arsev Umur/0000-0001-8857-6001},
Funding-Acknowledgement = {Scientific and Technological Research Council of Turkey (TUBITAK);
   Turkish Academic Network and Research Center (ULAKBIM)},
Funding-Text = {We would like to thank people working for The Scientific and
   Technological Research Council of Turkey (TUBITAK); the Turkish Academic
   Network and Research Center (ULAKBIM) for their support; Filiz Menguc
   and Ebru Aydn for the processes of designing the survey; Murat Koreke
   for the distribution of survey via LimeSurvey; and M. Mirat Satolu,
   director of ULAKBIM, for his support on matters relating to
   administrative processes.},
Number-of-Cited-References = {63},
Times-Cited = {1},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {32},
Journal-ISO = {IFLA J.-Int. Fed. Libr. Assoc.},
Doc-Delivery-Number = {QY5PI},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000533012500001},
DA = {2024-01-15},
}

@article{ WOS:000477727500008,
Author = {Tenenbaum, Jessica D. and Bhuvaneshwar, Krithika and Gagliardi, Jane P.
   and Fultz Hollis, Kate and Jia, Peilin and Ma, Liang and Nagarajan,
   Radhakrishnan and Rakesh, Gopalkumar and Subbian, Vignesh and
   Visweswaran, Shyam and Zhao, Zhongming and Rozenblit, Leon},
Title = {Translational bioinformatics in mental health: open access data sources
   and computational biomarker discovery},
Journal = {BRIEFINGS IN BIOINFORMATICS},
Year = {2019},
Volume = {20},
Number = {3},
Pages = {842-856},
Month = {MAY},
Abstract = {Mental illness is increasingly recognized as both a significant cost to
   society and a significant area of opportunity for biological
   breakthrough. As -omics and imaging technologies enable researchers to
   probe molecular and physiological underpinnings of multiple diseases,
   opportunities arise to explore the biological basis for behavioral
   health and disease. From individual investigators to large international
   consortia, researchers have generated rich data sets in the area of
   mental health, including genomic, transcriptomic, metabolomic,
   proteomic, clinical and imaging resources. General data repositories
   such as the Gene Expression Omnibus (GEO) and Database of Genotypes and
   Phenotypes (dbGaP) and mental health (MH)-specific initiatives, such as
   the Psychiatric Genomics Consortium, MH Research Network and PsychENCODE
   represent a wealth of information yet to be gleaned. At the same time,
   novel approaches to integrate and analyze data sets are enabling
   important discoveries in the area of mental and behavioral health. This
   review will discuss and catalog into an organizing framework the
   increasingly diverse set of MH data resources available, using
   schizophrenia as a focus area, and will describe novel and integrative
   approaches to molecular biomarker discovery that make use of mental
   health data.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Tenenbaum, JD (Corresponding Author), Duke Univ, Sch Med, Dept Biostat \& Bioinformat, Durham, NC 27708 USA.
   Tenenbaum, Jessica D., Duke Univ, Sch Med, Dept Biostat \& Bioinformat, Translat Biomed Informat, Durham, NC 27706 USA.
   Tenenbaum, Jessica D., Amer Med Informat Assoc AMIA, Mental Hlth Informat Working Grp, Bethesda, MD USA.
   Bhuvaneshwar, Krithika, Georgetown Univ, Innovat Ctr Biomed Informat ICBI, Washington, DC 20057 USA.
   Gagliardi, Jane P., Duke Univ, Sch Med, Psychiat \& Behav Sci, Durham, NC 27706 USA.
   Gagliardi, Jane P., Duke Univ, Sch Med, Med, Durham, NC 27706 USA.
   Fultz Hollis, Kate, Oregon Hlth \& Sci Univ, Dept Biomed Informat \& Clin Epidemiol, Portland, OR 97201 USA.
   Jia, Peilin; Zhao, Zhongming, Univ Texas Hlth Sci Ctr Houston, Sch Biomed Informat, Ctr Precis Hlth, Houston, TX 77030 USA.
   Jia, Peilin; Zhao, Zhongming, Bioinformat \& Syst Med Lab, Houston, TX USA.
   Ma, Liang, Univ Texas Hlth Sci Ctr Houston, Sch Biomed Informat, Ctr Precis Hlth, Bioinformat \& Syst Med Lab BSML, Houston, TX 77030 USA.
   Nagarajan, Radhakrishnan, Univ Kentucky, Coll Med, Biomed Informat, Lexington, KY 40506 USA.
   Rakesh, Gopalkumar, Duke Univ, Med Ctr, Dept Psychiat, Durham, NC 27706 USA.
   Subbian, Vignesh, Univ Arizona, Dept Biomed Engn, Tucson, AZ 85721 USA.
   Subbian, Vignesh, Univ Arizona, Dept Syst \& Ind Engn, Tucson, AZ 85721 USA.
   Visweswaran, Shyam, Univ Pittsburgh, Biomed Informat, Pittsburgh, PA 15260 USA.
   Visweswaran, Shyam, Univ Pittsburgh, Intelligent Syst Program, Pittsburgh, PA 15260 USA.
   Visweswaran, Shyam, Univ Pittsburgh, Dept Biomed Informat, Clin Informat, Pittsburgh, PA 15260 USA.
   Visweswaran, Shyam, Univ Pittsburgh, Ctr Clin Res Informat, Pittsburgh, PA 15260 USA.
   Visweswaran, Shyam, Univ Pittsburgh, Clin \& Translat Sci Inst, Biomed Informat Core, Pittsburgh, PA 15260 USA.
   Zhao, Zhongming, Univ Texas Hlth Sci Ctr Houston, Precis Hlth, Houston, TX 77030 USA.
   Rozenblit, Leon, Prometheus Res LLC, New Haven, CT USA.
   Rozenblit, Leon, Simons Simplex Collect, New Haven, CT USA.
   Rozenblit, Leon, Autism Biomarker Consortium Clin Trials, New Haven, CT USA.},
DOI = {10.1093/bib/bbx157},
ISSN = {1467-5463},
EISSN = {1477-4054},
Keywords = {translational bioinformatics; mental health; open access; biomarker
   discovery},
Keywords-Plus = {GENOME-WIDE ASSOCIATION; RESEARCH DOMAIN CRITERIA; BIPOLAR DISORDER;
   COMMON VARIANTS; GENE-EXPRESSION; SCHIZOPHRENIA RISK; CONFERRING RISK;
   HUMAN BRAIN; GWAS; REVEALS},
Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Mathematical \& Computational Biology},
Author-Email = {jessie.tenenbaum@duke.edu},
Affiliations = {Duke University; Georgetown University; Duke University; Duke
   University; Oregon Health \& Science University; University of Texas
   System; University of Texas Health Science Center Houston; University of
   Texas System; University of Texas Health Science Center Houston;
   University of Kentucky; Duke University; University of Arizona;
   University of Arizona; Pennsylvania Commonwealth System of Higher
   Education (PCSHE); University of Pittsburgh; Pennsylvania Commonwealth
   System of Higher Education (PCSHE); University of Pittsburgh;
   Pennsylvania Commonwealth System of Higher Education (PCSHE); University
   of Pittsburgh; Pennsylvania Commonwealth System of Higher Education
   (PCSHE); University of Pittsburgh; Pennsylvania Commonwealth System of
   Higher Education (PCSHE); University of Pittsburgh; University of Texas
   System; University of Texas Health Science Center Houston},
ResearcherID-Numbers = {Ma, Liang/G-2576-2017
   Fultz-Hollis, Kate/GYR-0175-2022
   },
ORCID-Numbers = {Ma, Liang/0000-0001-7034-9011
   Fultz Hollis, Kate/0000-0002-4668-6015
   Subbian, Vignesh/0000-0001-9974-8382
   B, Krithika/0000-0003-4015-7056},
Funding-Acknowledgement = {National Institutes of Health {[}UL1TR001117, R01LM012095, R01LM012806]},
Funding-Text = {The National Institutes of Health (grant numbers UL1TR001117 to J.D.T.,
   R01LM012095 to S.V. and R01LM012806 to P.J. and Z.Z.).},
Number-of-Cited-References = {105},
Times-Cited = {8},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {14},
Journal-ISO = {Brief. Bioinform.},
Doc-Delivery-Number = {IM1DA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000477727500008},
OA = {Green Submitted, hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000826501600001,
Author = {Jenkins, Tia and Persaud, Bhaleka D. and Cowger, Win and Szigeti, Kathy
   and Roche, Dominique G. and Clary, Erin and Slowinski, Stephanie and
   Lei, Benjamin and Abeynayaka, Amila and Nyadjro, Ebenezer S. and Maes,
   Thomas and Hampton, Leah Thornton and Bergmann, Melanie and Aherne,
   Julian and Mason, Sherri A. and Honek, John F. and Rezanezhad, Fereidoun
   and Lusher, Amy L. and Booth, Andy M. and Smith, Rodney D. L. and Van
   Cappellen, Philippe},
Title = {Current State of Microplastic Pollution Research Data: Trends in
   Availability and Sources of Open Data},
Journal = {FRONTIERS IN ENVIRONMENTAL SCIENCE},
Year = {2022},
Volume = {10},
Month = {JUN 30},
Abstract = {The rapid growth in microplastic pollution research is influencing
   funding priorities, environmental policy, and public perceptions of
   risks to water quality and environmental and human health. Ensuring that
   environmental microplastics research data are findable, accessible,
   interoperable, and reusable (FAIR) is essential to inform policy and
   mitigation strategies. We present a bibliographic analysis of data
   sharing practices in the environmental microplastics research community,
   highlighting the state of openness of microplastics data. A stratified
   (by year) random subset of 785 of 6,608 microplastics articles indexed
   in Web of Science indicates that, since 2006, less than a third (28.5\%)
   contained a data sharing statement. These statements further show that
   most often, the data were provided in the articles' supplementary
   material (38.8\%) and only 13.8\% via a data repository. Of the 279
   microplastics datasets found in online data repositories, 20.4\%
   presented only metadata with access to the data requiring additional
   approval. Although increasing, the rate of microplastic data sharing
   still lags behind that of publication of peer-reviewed articles on
   environmental microplastics. About a quarter of the repository data
   originated from North America (12.8\%) and Europe (13.4\%). Marine and
   estuarine environments are the most frequently sampled systems (26.2\%);
   sediments (18.8\%) and water (15.3\%) are the predominant media. Of the
   available datasets accessible, 15.4\% and 18.2\% do not have adequate
   metadata to determine the sampling location and media type,
   respectively. We discuss five recommendations to strengthen data sharing
   practices in the environmental microplastic research community.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Jenkins, T (Corresponding Author), Univ Waterloo, Dept Earth \& Environm Sci, Waterloo, ON, Canada.
   Jenkins, Tia; Persaud, Bhaleka D.; Slowinski, Stephanie; Lei, Benjamin; Rezanezhad, Fereidoun; Van Cappellen, Philippe, Univ Waterloo, Dept Earth \& Environm Sci, Waterloo, ON, Canada.
   Cowger, Win, Moore Inst Plast Pollut Res, Long Beach, CA USA.
   Szigeti, Kathy, Univ Waterloo, Davis Ctr Lib, Waterloo, ON, Canada.
   Roche, Dominique G., Carleton Univ, Dept Biol, Ottawa, ON, Canada.
   Roche, Dominique G., Univ Neuchatel, Inst Biol, Neuchatel, Switzerland.
   Clary, Erin, Digital Res Alliance Canada, Ottawa, ON, Canada.
   Abeynayaka, Amila, Inst Global Environm Strategies IGES, Kanagawa, Japan.
   Nyadjro, Ebenezer S., NCEI, NOAA, Stennis Space Ctr, Starkville, MS USA.
   Nyadjro, Ebenezer S., Mississippi State Univ, Northern Gulf Inst, Stennis Space Ctr, Starkville, MS USA.
   Maes, Thomas, GRID Arendal, Arendal, Norway.
   Hampton, Leah Thornton, Southern Calif Coastal Water Res Project SCCWRP, Costa Mesa, CA USA.
   Bergmann, Melanie, Alfred Wegener Inst, Helmholtz Zentrum Polar \& Meeresforsch, Bremerhaven, Germany.
   Aherne, Julian, Trent Univ, Sch Environm, Peterborough, ON, Canada.
   Mason, Sherri A., Penn State Univ, Behrend Coll, Erie, PA USA.
   Honek, John F.; Smith, Rodney D. L., Univ Waterloo, Dept Chem, Waterloo, ON, Canada.
   Lusher, Amy L., Norwegian Inst Water Res, Oslo, Norway.
   Booth, Andy M., SINTEF Ocean, Trondheim, Norway.},
DOI = {10.3389/fenvs.2022.912107},
Article-Number = {912107},
EISSN = {2296-665X},
Keywords = {microplastics; bibliometric analysis; data repository; data availability
   statement; data management; data sharing; environmental research;
   plastic},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Environmental Sciences},
Author-Email = {t4jenkins@uwaterloo.ca},
Affiliations = {University of Waterloo; University of Waterloo; Carleton University;
   University of Neuchatel; National Oceanic Atmospheric Admin (NOAA) -
   USA; Mississippi State University; Helmholtz Association; Alfred Wegener
   Institute, Helmholtz Centre for Polar \& Marine Research; Trent
   University; Pennsylvania Commonwealth System of Higher Education
   (PCSHE); Pennsylvania State University; University of Waterloo;
   Norwegian Institute for Water Research (NIVA); SINTEF},
ResearcherID-Numbers = {Cowger, Win/G-2483-2018
   Smith, Rodney/K-6870-2016
   Lusher, Amy L./Q-3483-2018
   Bergmann, Melanie/H-3347-2015},
ORCID-Numbers = {Cowger, Win/0000-0001-9226-3104
   Smith, Rodney/0000-0003-1209-9653
   Lusher, Amy L./0000-0003-0539-2974
   Slowinski, Stephanie/0000-0001-5090-441X
   Szigeti, Kathy/0000-0003-1790-9790
   Maes, Thomas/0000-0002-1282-8871
   Bergmann, Melanie/0000-0001-5212-9808},
Funding-Acknowledgement = {NSERC/ECCC Alliance Grants - Plastics science for a cleaner future
   program {[}ALLRP 558435-20]; Canada First Research Excellence Fund
   Global Water Futures Programme; McPike Zima Charitable; PoF IV program
   Changing Earth - Sustaining our Future Topic 6.4 of the German Helmholtz
   Association; Research Council of Norway {[}301157, 295174, 312262];
   Early-Career Research Fellowship from the Gulf Research Program of the
   US National Academies of Sciences, Engineering, and Medicine
   {[}2000012639]; European Unions Horizon 2020 Coordination and Support
   Action programme {[}101003805]; Union Horizon 2020 research and
   innovation programme under Marie Sklodowska-Curie grant
   {[}838237-OPTIMISE]},
Funding-Text = {This work was primarily funded by the NSERC/ECCC Alliance Grants -
   Plastics science for a cleaner future program (Grant Agreement \#: ALLRP
   558435-20). Additional funding support is also acknowledged from the
   following: the Canada First Research Excellence Fund Global Water
   Futures Programme, the McPike Zima Charitable, the PoF IV program
   Changing Earth - Sustaining our Future Topic 6.4 of the German Helmholtz
   Association, the Research Council of Norway projects REVEAL (Grant
   agreement \#. 301157), ANDROMEDA (Grant agreement \# 312262), MicroLEACH
   (Grant agreement \#. 295174), the Early-Career Research Fellowship from
   the Gulf Research Program of the US National Academies of Sciences,
   Engineering, and Medicine (Grant agreement \# 2000012639), European
   Unions Horizon 2020 Coordination and Support Action programme under
   Grant agreement 101003805 (EUROqCHARM), and the Union Horizon 2020
   research and innovation programme under Marie Sklodowska-Curie grant
   agreement no. 838237-OPTIMISE.},
Number-of-Cited-References = {57},
Times-Cited = {13},
Usage-Count-Last-180-days = {11},
Usage-Count-Since-2013 = {33},
Journal-ISO = {Front. Environ. Sci.},
Doc-Delivery-Number = {2Z3SG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000826501600001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:001030033800078,
Author = {Boogaard, Hendrik and Pratihast, Arun Kumar and Bayas, Juan Carlos Laso
   and Karanam, Santosh and Fritz, Steffen and Van Tricht, Kristof and
   Degerickx, Jeroen and Gilliams, Sven},
Title = {Building a community-based open harmonised reference data repository for
   global crop mapping},
Journal = {PLOS ONE},
Year = {2023},
Volume = {18},
Number = {7},
Month = {JUL 13},
Abstract = {Reference data is key to produce reliable crop type and cropland maps.
   Although research projects, national and international programs as well
   as local initiatives constantly gather crop related reference data,
   finding, collecting, and harmonizing data from different sources is a
   challenging task. Furthermore, ethical, legal, and consent-related
   restrictions associated with data sharing represent a common dilemma
   faced by international research projects. We address these dilemmas by
   building a community-based, open, harmonised reference data repository
   at global extent, ready for model training or product validation. Our
   repository contains data from different sources such as the Group on
   Earth Observations Global Agricultural Monitoring Initiative (GEOGLAM)
   Joint Experiment for Crop Assessment and Monitoring (JECAM) sites, the
   Radiant MLHub, the Future Harvest (CGIAR) centers, the National
   Aeronautics and Space Administration Food Security and Agriculture
   Program (NASA Harvest), the International Institute for Applied Systems
   Analysis (IIASA) citizen science platforms (LACO-Wiki and Geo-Wiki), as
   well as from individual project contributions. Data of 2016 onwards were
   collected, harmonised, and annotated. The data sets spatial, temporal,
   and thematic quality were assessed applying rules developed in this
   research. Currently, the repository holds around 75 million harmonised
   observations with standardized metadata of which a large share is
   available to the public. The repository, funded by ESA through the
   WorldCereal project, can be used for either the calibration of image
   classification deep learning algorithms or the validation of Earth
   Observation generated products, such as global cropland extent and maize
   and wheat maps. We recommend continuing and institutionalizing this
   reference data initiative e.g. through GEOGLAM, and encouraging the
   community to publish land cover and crop type data following the open
   science and open data principles.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Boogaard, H (Corresponding Author), Wageningen Univ \& Res, Wageningen Environm Res WENR, Wageningen, Netherlands.
   Boogaard, Hendrik; Pratihast, Arun Kumar, Wageningen Univ \& Res, Wageningen Environm Res WENR, Wageningen, Netherlands.
   Bayas, Juan Carlos Laso; Karanam, Santosh; Fritz, Steffen, Int Inst Appl Syst Anal IIASA, Laxenburg, Austria.
   Van Tricht, Kristof; Degerickx, Jeroen; Gilliams, Sven, Vlaamse Inst Technol Onderzoek VITO, Mol, Belgium.},
DOI = {10.1371/journal.pone.0287731},
Article-Number = {e0287731},
ISSN = {1932-6203},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {hendrik.boogaard@wur.nl},
Affiliations = {Wageningen University \& Research; International Institute for Applied
   Systems Analysis (IIASA)},
ORCID-Numbers = {Karanam, Santosh/0000-0001-9171-3193
   Degerickx, Jeroen/0000-0001-9022-9623
   Pratihast, Arun/0000-0003-3131-8399},
Funding-Acknowledgement = {European Space Agency (ESA) WorldCereal project {[}4000130569/20/I-NB];
   European Union {[}101059548]},
Funding-Text = {The work has received funding from the European Space Agency (ESA)
   WorldCereal project under the project number No. 4000130569/20/I-NB and
   by the Open Earth Monitor (OEMF) project, a project funded by the
   European Union's Horizon Europe research and innovation programme under
   grant agreement No.-101059548. ESA defined the general WorldCereal
   project specifications which included the set-up and building of a
   reference data repository as one of the main components of the
   WorldCereal system.},
Number-of-Cited-References = {37},
Times-Cited = {1},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {3},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {M4PA9},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001030033800078},
OA = {gold, Green Accepted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000368069900008,
Author = {Nicotri, Stefano and Tinelli, Eufemia and Amoroso, Nicola and Garuccio,
   Elena and Bellotti, Roberto},
Title = {Complex networks and public funding: the case of the 2007-2013 Italian
   program},
Journal = {EPJ DATA SCIENCE},
Year = {2015},
Volume = {4},
Number = {1},
Month = {DEC},
Abstract = {In this paper we apply techniques of complex network analysis to data
   sources representing public funding programs and discuss the importance
   of the considered indicators for program evaluation. Starting from the
   Open Data repository of the 2007-2013 Italian Program Programma
   Operativo Nazionale `Ricerca e Competitivita' (PON R\&C), we build a set
   of data models and perform network analysis over them. We discuss the
   obtained experimental results outlining interesting new perspectives
   that emerge from the application of the proposed methods to the
   socio-economical evaluation of funded programs.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Nicotri, S (Corresponding Author), Ist Nazl Fis Nucl, Sez Bari, Via Orabona 4, I-70125 Bari, Italy.
   Nicotri, Stefano; Amoroso, Nicola; Bellotti, Roberto, Ist Nazl Fis Nucl, Sez Bari, I-70125 Bari, Italy.
   Tinelli, Eufemia; Amoroso, Nicola; Bellotti, Roberto, Univ Bari A Moro, Dipartimento Interateneo Fis M Merlin, I-70125 Bari, Italy.
   Tinelli, Eufemia, Comune Bari Ripartiz Innovaz Tecnol Sistemi Infor, I-70122 Bari, Italy.
   Garuccio, Elena, Univ Siena, Dipartimento Sci Fis Ambiente \& Terra, I-53100 Siena, Italy.},
DOI = {10.1140/epjds/s13688-015-0047-z},
Article-Number = {8},
EISSN = {2193-1127},
Keywords = {public funding; open data; complex networks; program evaluation},
Keywords-Plus = {STATISTICAL-MECHANICS; SEARCH},
Research-Areas = {Mathematics; Mathematical Methods In Social Sciences},
Web-of-Science-Categories  = {Mathematics, Interdisciplinary Applications; Social Sciences,
   Mathematical Methods},
Author-Email = {stefano.nicotri@ba.infn.it},
Affiliations = {Istituto Nazionale di Fisica Nucleare (INFN); Universita degli Studi di
   Bari Aldo Moro; University of Siena},
ResearcherID-Numbers = {Bellotti, Roberto/HTM-5191-2023
   Nicotri, Stefano/A-1185-2012
   },
ORCID-Numbers = {Bellotti, Roberto/0000-0003-3198-2708
   Nicotri, Stefano/0000-0003-2707-1098
   Amoroso, Nicola/0000-0003-0211-0783},
Funding-Acknowledgement = {Italian MIUR {[}PON PRISMA Cod. PON04a2\_A]},
Funding-Text = {We thank N Coniglio for valuable suggestions and discussions. SN thanks
   R Anglani and V Mariani for discussions. SN, and NA acknowledge funding
   by the Italian MIUR grant PON PRISMA Cod. PON04a2\_A. ET acknowledges
   partial funding by the Italian MIUR grant PON PRISMA Cod. PON04a2\_A.},
Number-of-Cited-References = {41},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {13},
Journal-ISO = {EPJ Data Sci.},
Doc-Delivery-Number = {DA8QE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000368069900008},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000618539400006,
Author = {Allen, Scott T. and Berghuijs, Wouter R.},
Title = {A need for incentivizing field hydrology, especially in an era of open
   data: discussion of ``The role of experimental work in hydrological
   sciences - insights from a community survey{''} (Reprinted from
   HYDROLOGICAL SCIENCES JOURNAL-JOURNAL DES SCIENCES HYDROLOGIQUES, vol
   63, pg 1262-1265, 2018)},
Journal = {HYDROLOGICAL SCIENCES JOURNAL},
Year = {2020},
Volume = {65},
Number = {2},
Pages = {1262-1265},
Abstract = {The sharing of data and collection of new data are both essential, but
   they are not inherently complementary. When data are openly available,
   researchers may be motivated to use those data rather than collect more
   because field work has costs and risks. The competitive advantage to
   those who do not put resources towards fieldwork may discourage field
   hydrology. Allocating efforts towards generating field data, which
   benefits hydrological sciences, is not necessarily best for individual
   hydrologists, especially in an era of open data. The objective of this
   work is to open a conversation on whether individuals' best interests
   may contrast with the community's desire for new observations. If the
   community wants new field observations, there is a need to consider the
   shifting balance of incentives and disincentives for pursuing field
   studies in hydrology.},
Publisher = {TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND},
Type = {Reprint},
Language = {English},
Affiliation = {Allen, ST (Corresponding Author), Swiss Fed Inst Technol, Dept Environm Syst Sci, Zurich, Switzerland.
   Allen, Scott T., Swiss Fed Inst Technol, Dept Environm Syst Sci, Zurich, Switzerland.},
ISSN = {0262-6667},
EISSN = {2150-3435},
Keywords = {fieldwork; open-access data; data repositories; social dilemma;
   experimental hydrology},
Keywords-Plus = {COOPERATION; TRAGEDY},
Research-Areas = {Water Resources},
Web-of-Science-Categories  = {Water Resources},
Author-Email = {allensc@ethz.ch},
Affiliations = {Swiss Federal Institutes of Technology Domain; ETH Zurich},
Number-of-Cited-References = {26},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Hydrol. Sci. J.},
Doc-Delivery-Number = {QH8RJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000618539400006},
DA = {2024-01-15},
}

@article{ WOS:000304920200002,
Author = {Csordas, Attila and Ovelleiro, David and Wang, Rui and Foster, Joseph M.
   and Rios, Daniel and Vizcaino, Juan Antonio and Hermjakob, Henning},
Title = {PRIDE: Quality control in a proteomics data repository},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2012},
Month = {MAR 20},
Abstract = {The PRoteomics IDEntifications (PRIDE) database is a large public
   proteomics data repository, containing over 270 million mass spectra (by
   November 2011). PRIDE is an archival database, providing the proteomics
   data supporting specific scientific publications in a computationally
   accessible manner. While PRIDE faces rapid increases in data deposition
   size as well as number of depositions, the major challenge is to ensure
   a high quality of data depositions in the context of highly diverse
   proteomics work flows and data representations. Here, we describe the
   PRIDE curation pipeline and its practical application in quality control
   of complex data depositions.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Csordas, A (Corresponding Author), European Bioinformat Inst EBI, EMBL Outstn, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Csordas, Attila; Ovelleiro, David; Wang, Rui; Foster, Joseph M.; Rios, Daniel; Vizcaino, Juan Antonio; Hermjakob, Henning, European Bioinformat Inst EBI, EMBL Outstn, Cambridge CB10 1SD, England.},
DOI = {10.1093/database/bas004},
Article-Number = {bas004},
ISSN = {1758-0463},
Keywords-Plus = {STANDARD},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {acsordas@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL)},
ResearcherID-Numbers = {Hermjakob, Henning/AFM-3497-2022
   Vizcaino, Juan Antonio/C-3691-2009
   },
ORCID-Numbers = {Hermjakob, Henning/0000-0001-8479-0262
   Vizcaino, Juan Antonio/0000-0002-3905-4335
   Ovelleiro, David/0000-0002-9415-2229},
Funding-Acknowledgement = {Wellcome Trust {[}WT085949MA]; EMBL; EU {[}202272]; ProteomeXchange
   {[}260558]},
Funding-Text = {Wellcome Trust (grant number WT085949MA to The PRIDE database); EMBL
   core funding; EU FP7 LipidomicNet (grant number 202272 to J.A.V.);
   ProteomeXchange (grant number 260558). Funding for open access charge:
   Wellcome Trust (grant number WT085949MA to The PRIDE database).},
Number-of-Cited-References = {14},
Times-Cited = {29},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Database},
Doc-Delivery-Number = {954BO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000304920200002},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000298601300100,
Author = {Gilsenan, Jane Mabey and Cooley, John and Bowyer, Paul},
Title = {C<i>A</i>DRE: the Central <i>Aspergillus</i> Data REpository 2012},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2012},
Volume = {40},
Number = {D1},
Pages = {D660-D666},
Month = {JAN},
Abstract = {The Central Aspergillus Data REpository (CADRE;
   http://www.cadre-genomes.org.uk) is a public resource for genomic data
   extracted from species of Aspergillus. It provides an array of online
   tools for searching and visualising features of this significant fungal
   genus. CADRE arose from a need within the medical community to
   understand the human pathogen Aspergillus fumigatus. Due to the paucity
   of Aspergillus genomic resources 10 years ago, the long-term goal of
   this project was to collate and maintain Aspergillus genomes as they
   became available. Since our first release in 2004, the resource has
   expanded to encompass annotated sequence for eight other Aspergilli and
   provides much needed support to the international Aspergillus research
   community. Recent developments, however, in sequencing technology are
   creating a vast amount of genomic data and, as a result, we shortly
   expect a tidal wave of Aspergillus data. In preparation for this, we
   have upgraded the database and software suite. This not only enables
   better management of more complex data sets, but also improves
   annotation by providing access to genome comparison data and the
   integration of high-throughput data.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Gilsenan, JM (Corresponding Author), Univ Manchester, Sch Translat Med, Manchester M23 9LT, Lancs, England.
   Gilsenan, Jane Mabey; Bowyer, Paul, Univ Manchester, Sch Translat Med, Manchester M23 9LT, Lancs, England.
   Cooley, John, Univ S Manchester Hosp, Univ IT Serv, R\&D Dept, Manchester M23 9LT, Lancs, England.},
DOI = {10.1093/nar/gkr971},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENOME; FUMIGATUS; GENE; ITRACONAZOLE; DUPLICATION; ANNOTATION;
   NIDULANS; SEQUENCE; RESOURCE; ENSEMBL},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {jane.gilsenan@manchester.ac.uk},
Affiliations = {University of Manchester; Wythenshawe Hospital NHS Foundation Trust;
   Wythenshawe Hospital},
ResearcherID-Numbers = {Bowyer, Paul/O-1632-2017
   },
ORCID-Numbers = {Bowyer, Paul/0000-0002-2056-2778
   bowyer, paul/0000-0002-1083-9286},
Funding-Acknowledgement = {SYBARIS project; EU {[}242220]},
Funding-Text = {SYBARIS project; EU Framework Programme 7 Collaborative Project (grant
   number 242220). Funding for open access charge: SYBARIS, FP7 project
   (grant number 242220).},
Number-of-Cited-References = {35},
Times-Cited = {31},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {869MD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000298601300100},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000366151000015,
Author = {Karayanidis, Frini and Keuken, Max C. and Wong, Aaron and Rennie, Jaime
   L. and de Hollander, Gilles and Cooper, Patrick S. and Fulham, W. Ross
   and Lenroot, Rhoshel and Parsons, Mark and Phillips, Natalie and Michie,
   Patricia T. and Forstmann, Birte U.},
Title = {The Age-ility Project (Phase 1): Structural and functional imaging and
   electrophysiological data repository},
Journal = {NEUROIMAGE},
Year = {2016},
Volume = {124},
Number = {B, SI},
Pages = {1137-1142},
Month = {JAN 1},
Abstract = {Our understanding of the complex interplay between structural and
   functional organisation of brain networks is being advanced by the
   development of novel multi-modal analyses approaches. The Age-ility
   Project (Phase 1) data repository offers open access to structural MRI,
   diffusion MAI, and resting-state fMRI scans, as well as resting-state
   EEG recorded from the same community participants (n = 131, 15-35 y, 66
   male). Raw imaging and electrophysiological data as well as essential
   demographics are made available via the NITRC website. All data have
   been reviewed for artifacts using a rigorous quality control protocol
   and detailed case notes are provided. (C) 2015 Published by Elsevier
   Inc.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Karayanidis, F (Corresponding Author), Univ Newcastle, Sch Psychol, Funct Neuroimaging Lab, Callaghan, NSW 2308, Australia.
   Karayanidis, Frini; Wong, Aaron; Rennie, Jaime L.; Cooper, Patrick S.; Fulham, W. Ross; Michie, Patricia T., Univ Newcastle, Sch Psychol, Funct Neuroimaging Lab, Callaghan, NSW 2308, Australia.
   Keuken, Max C.; de Hollander, Gilles; Forstmann, Birte U., Univ Amsterdam, Amsterdam Brain \& Cognit, NL-1018 VZ Amsterdam, Netherlands.
   Lenroot, Rhoshel, Univ New S Wales, Neurosci Res Australia, Sydney, NSW 2052, Australia.
   Parsons, Mark, Univ Newcastle, Sch Med \& Publ Hlth, Callaghan, NSW 2308, Australia.
   Phillips, Natalie, Concordia Univ, Dept Psychol, Montreal, PQ, Canada.
   Keuken, Max C.; de Hollander, Gilles; Forstmann, Birte U., Univ Amsterdam, Dept Psychol, NL-1018 VZ Amsterdam, Netherlands.
   Karayanidis, Frini; Wong, Aaron; Rennie, Jaime L.; Cooper, Patrick S.; Fulham, W. Ross; Parsons, Mark; Michie, Patricia T., Univ Newcastle, Prior Res Ctr Translat Neurosci \& Mental Hlth, Callaghan, NSW 2308, Australia.
   Karayanidis, Frini; Wong, Aaron; Rennie, Jaime L.; Cooper, Patrick S.; Fulham, W. Ross; Parsons, Mark; Michie, Patricia T., Univ Newcastle, Hunter Med Res Inst, Callaghan, NSW 2308, Australia.},
DOI = {10.1016/j.neuroimage.2015.04.047},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords-Plus = {REGISTRATION; MRI},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {Frini.Karayanidis@newcastle.edu.au},
Affiliations = {University of Newcastle; University of Amsterdam; University of New
   South Wales Sydney; Neuroscience Research Australia; University of
   Newcastle; Concordia University - Canada; University of Amsterdam;
   University of Newcastle; Hunter Medical Research Institute; University
   of Newcastle},
ResearcherID-Numbers = {Forstmann, Birte/AAS-8515-2020
   Karayanidis, Frini/I-9269-2012
   },
ORCID-Numbers = {Karayanidis, Frini/0000-0002-3317-9954
   Wong, Aaron Seng Wai/0000-0001-8424-3939
   Keuken, Max/0000-0002-9703-9125
   de Hollander, Gilles/0000-0003-1988-5091
   Cooper, Patrick/0000-0002-0222-8514},
Funding-Acknowledgement = {Australian Research Council Discovery Project grant {[}ARC-DP
   120100340]; Australian Postgraduate Award; European Research Council
   {[}ERC-2012-StG-313481]},
Funding-Text = {This work was supported by an Australian Research Council Discovery
   Project grant (ARC-DP 120100340) to Karayanidis, Forstmann, Michie,
   Parsons, Wagenmakers, Phillips, Lenroot. Cooper and Rennie were
   supported by an Australian Postgraduate Award. This research line is
   financially supported by the European Research Council (BUF)
   (ERC-2012-StG-313481). We thank Jameen Arms, head radiographer at the
   Calvary Mater Hospital, for his team's support with imaging, Tony Kemp
   and Gavin Cooper for technical support, and Elise Mansfield, Renate
   Thienel, Vanessa Case, Paul Garrett, Natalie Lantry, Olivia Whalen,
   Samantha Allen, Montana Hunter, Laura Williamson, Courtney Phillips,
   Cathryn Mackenzie and Patrick Skippen for their contribution to
   recruitment data collection, data entry and quality control.},
Number-of-Cited-References = {22},
Times-Cited = {12},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {CY1FB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000366151000015},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000716974500001,
Author = {Katikou, Panagiota},
Title = {Digital Technologies and Open Data Sources in Marine Biotoxins' Risk
   Analysis: The Case of Ciguatera Fish Poisoning},
Journal = {TOXINS},
Year = {2021},
Volume = {13},
Number = {10},
Month = {OCT},
Abstract = {Currently, digital technologies influence information dissemination in
   all business sectors, with great emphasis put on exploitation
   strategies. Public administrations often use information systems and
   establish open data repositories, primarily supporting their operation
   but also serving as data providers, facilitating decision-making. As
   such, risk analysis in the public health sector, including food safety
   authorities, often relies on digital technologies and open data sources.
   Global food safety challenges include marine biotoxins (MBs), being
   contaminants whose mitigation largely depends on risk analysis.
   Ciguatera Fish Poisoning (CFP), in particular, is a MB-related seafood
   intoxication attributed to the consumption of fish species that are
   prone to accumulate ciguatoxins. Historically, CFP occurred endemically
   in tropical/subtropical areas, but has gradually emerged in temperate
   regions, including European waters, necessitating official policy
   adoption to manage the potential risks. Researchers and policy-makers
   highlight scientific data inadequacy, under-reporting of outbreaks and
   information source fragmentation as major obstacles in developing CFP
   mitigation strategies. Although digital technologies and open data
   sources provide exploitable scientific information for MB risk analysis,
   their utilization in counteracting CFP-related hazards has not been
   addressed to date. This work thus attempts to answer the question,
   ``What is the current extent of digital technologies' and open data
   sources' utilization within risk analysis tasks in the MBs field,
   particularly on CFP? ``, by conducting a systematic literature review of
   the available scientific and grey literature. Results indicate that the
   use of digital technologies and open data sources in CFP is not
   negligible. However, certain gaps are identified regarding discrepancies
   in terminology, source fragmentation and a redundancy and downplay of
   social media utilization, in turn constituting a future research agenda
   for this under-researched topic.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Katikou, P (Corresponding Author), Minist Rural Dev \& Food, Directorate Gen Rural Dev, Directorate Res Innovat \& Educ, Hapsa \& Karatasou 1, Thessaloniki 54626, Greece.
   Katikou, Panagiota, Minist Rural Dev \& Food, Directorate Gen Rural Dev, Directorate Res Innovat \& Educ, Hapsa \& Karatasou 1, Thessaloniki 54626, Greece.},
DOI = {10.3390/toxins13100692},
Article-Number = {692},
EISSN = {2072-6651},
Keywords = {Ciguatera Fish Poisoning; digital technologies; open data; risk
   analysis; marine biotoxins},
Keywords-Plus = {SEA-SURFACE TEMPERATURES; FOOD SAFETY; INFORMATION-SYSTEMS;
   GAMBIERDISCUS; MANAGEMENT},
Research-Areas = {Food Science \& Technology; Toxicology},
Web-of-Science-Categories  = {Food Science \& Technology; Toxicology},
Author-Email = {pkatikou@otenet.gr},
ResearcherID-Numbers = {Katikou, Panagiota/H-4385-2019},
ORCID-Numbers = {Katikou, Panagiota/0000-0001-6050-5922},
Number-of-Cited-References = {75},
Times-Cited = {4},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {22},
Journal-ISO = {Toxins},
Doc-Delivery-Number = {WV1CK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000716974500001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000553831600001,
Author = {Guo, Xueqin and Chen, Fengzhen and Gao, Fei and Li, Ling and Liu, Ke and
   You, Lijin and Hua, Cong and Yang, Fan and Liu, Wanliang and Peng,
   Chunhua and Wang, Lina and Yang, Xiaoxia and Zhou, Feiyu and Tong,
   Jiawei and Cai, Jia and Li, Zhiyong and Wan, Bo and Zhang, Lei and Yang,
   Tao and Zhang, Minwen and Yang, Linlin and Yang, Yawen and Zeng, Wenjun
   and Wang, Bo and Wei, Xiaofeng and Xu, Xun},
Title = {CNSA: a data repository for archiving omics data},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2020},
Month = {JUL 23},
Abstract = {With the application and development of high-throughput sequencing
   technology in life and health sciences, massive multi-omics data brings
   the problem of efficient management and utilization. Database
   development and biocuration are the prerequisites for the reuse of these
   big data. Here, relying on China National GeneBank (CNGB), we present
   CNGB Sequence Archive (CNSA) for archiving omics data, including raw
   sequencing data and its further analyzed results which are organized
   into six objects, namely Project, Sample, Experiment, Run, Assembly and
   Variation at present. Moreover, CNSA has created a correlation model of
   living samples, sample information and analytical data on some projects.
   Both living samples and analytical data are directly correlated with the
   sample information. From either one, information or data of the other
   two can be obtained, so that all data can be traced throughout the life
   cycle from the living sample to the sample information to the analytical
   data. Complying with the data standards commonly used in the life
   sciences, CNSA is committed to building a comprehensive and curated data
   repository for storing, managing and sharing of omics data. We will
   continue to improve the data standards and provide free access to
   open-data resources for worldwide scientific communities to support
   academic research and the bio-industry.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Wei, XF; Xu, X (Corresponding Author), China Natl GeneBank, Shenzhen 518120, Peoples R China.
   Xu, X (Corresponding Author), BGI Shenzhen, Shenzhen 518083, Peoples R China.
   Xu, X (Corresponding Author), Guangdong Prov Key Lab Genome Read \& Write, Shenzhen 518120, Peoples R China.
   Guo, Xueqin; Chen, Fengzhen; Gao, Fei; Li, Ling; Liu, Ke; You, Lijin; Hua, Cong; Yang, Fan; Liu, Wanliang; Peng, Chunhua; Wang, Lina; Yang, Xiaoxia; Zhou, Feiyu; Tong, Jiawei; Cai, Jia; Li, Zhiyong; Wan, Bo; Zhang, Lei; Yang, Tao; Zhang, Minwen; Yang, Linlin; Yang, Yawen; Zeng, Wenjun; Wang, Bo; Wei, Xiaofeng; Xu, Xun, China Natl GeneBank, Shenzhen 518120, Peoples R China.
   Xu, Xun, BGI Shenzhen, Shenzhen 518083, Peoples R China.
   Xu, Xun, Guangdong Prov Key Lab Genome Read \& Write, Shenzhen 518120, Peoples R China.},
DOI = {10.1093/database/baaa055},
Article-Number = {baaa055},
ISSN = {1758-0463},
Keywords-Plus = {GENOMES},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {weixiaofeng@cngb.org
   xuxun@genomics.cn},
Affiliations = {Beijing Genomics Institute (BGI)},
ResearcherID-Numbers = {Jiang, Yuan/JED-3759-2023
   Guo, Xueqin/AAZ-9936-2020
   xun, xu/JGM-9272-2023
   Xu, Xun/AAI-6763-2020
   li, zy/HZM-1892-2023
   jiang, lei/IWE-1124-2023
   wei, xiao/ISB-6027-2023
   li, zhang/JHV-1750-2023
   Jiang, Tao/IWM-7503-2023
   liu, jingwen/JQW-9270-2023
   yang, xiao/HJI-7815-2023
   zhang, lin/IZQ-4870-2023
   },
ORCID-Numbers = {Xu, Xun/0000-0002-5338-5173
   Yang, Catherine/0000-0001-6040-6393
   yang, tao/0000-0003-4211-5183
   Guo, Xueqin/0000-0002-6325-0432},
Funding-Acknowledgement = {Guangdong Provincial Key Laboratory of Genome Read and Write
   {[}2017B030301011]},
Funding-Text = {This study was funded by the Guangdong Provincial Key Laboratory of
   Genome Read and Write (No. 2017B030301011).},
Number-of-Cited-References = {18},
Times-Cited = {172},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Database},
Doc-Delivery-Number = {MR8HI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000553831600001},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001134320700001,
Author = {Maghami, Iman and Morsy, Mohamed M. and Sadler, Jeffrey M. and
   Horsburgh, Jeffery S. and Dash, Pabitra K. and Choi, Youngdon and Chen,
   Kevin and Seul, Martin and Black, Scott and Tarboton, David G. and
   Goodall, Jonathan L.},
Title = {An extensible schema for capturing environmental model metadata:
   Implementation in the HydroShare online data repository},
Journal = {ENVIRONMENTAL MODELLING \& SOFTWARE},
Year = {2024},
Volume = {172},
Month = {JAN},
Abstract = {Model metadata can be used to document the specifications, inputs,
   provenance, and other important attributes of an environmental modeling
   application. An open challenge in creating a general model metadata
   schema is addressing the diversity of environmental models in a way that
   provides flexibility and scalability while maintaining a standard core.
   This paper presents a new model metadata schema design aimed at
   addressing this challenge. Specifically, we present an extensible
   metadata schema for describing what we call a model instance: a specific
   application of an environmental model. We implement the schema in the
   HydroShare online data repository and demonstrate how the schema can be
   used for the Soil and Water Assessment (SWAT) model.},
Publisher = {ELSEVIER SCI LTD},
Address = {125 London Wall, London, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Maghami, I (Corresponding Author), Univ Virginia, Dept Civil \& Environm Engn, 151 Engineers Way,POB 400747, Charlottesville, VA 22904 USA.
   Maghami, Iman; Goodall, Jonathan L., Univ Virginia, Dept Civil \& Environm Engn, Charlottesville, VA USA.
   Maghami, Iman, Brigham Young Univ, Dept Civil \& Construct Engn, Provo, UT USA.
   Morsy, Mohamed M., Cairo Univ, Irrigat \& Hydraul Engn Dept, Giza, Egypt.
   Sadler, Jeffrey M., Oklahoma State Univ, Dept Biosyst \& Agr Engn, Stillwater, OK USA.
   Horsburgh, Jeffery S.; Dash, Pabitra K.; Tarboton, David G., Utah State Univ, Dept Civil \& Environm Engn, Utah Water Res Lab, Logan, UT USA.
   Choi, Youngdon, K Water Res Inst, R\&D Management Dept, AI Res Lab, Daejeon, South Korea.
   Chen, Kevin, Univ Virginia, Dept Comp Sci, Charlottesville, VA USA.
   Seul, Martin; Black, Scott, Consortium Univ Advancement Hydrol Sci Inc, Arlington, MA USA.
   Maghami, Iman, Univ Virginia, Dept Civil \& Environm Engn, 151 Engineers Way,POB 400747, Charlottesville, VA 22904 USA.},
DOI = {10.1016/j.envsoft.2023.105895},
EarlyAccessDate = {DEC 2023},
Article-Number = {105895},
ISSN = {1364-8152},
EISSN = {1873-6726},
Keywords = {Environmental modeling; Hydrologic modeling; Standard metadata schema;
   Model metadata; Linked data; Reproducibility; HydroShare; Open science;
   Web -based repositories},
Keywords-Plus = {COMPUTATIONAL HYDROLOGY; REPRODUCIBILITY; EXAMPLE; DESIGN},
Research-Areas = {Computer Science; Engineering; Environmental Sciences \& Ecology; Water
   Resources},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Engineering,
   Environmental; Environmental Sciences; Water Resources},
Author-Email = {im3vp@virginia.edu},
Affiliations = {University of Virginia; Brigham Young University; Egyptian Knowledge
   Bank (EKB); Cairo University; Oklahoma State University System; Oklahoma
   State University - Stillwater; Utah System of Higher Education; Utah
   State University; University of Virginia; University of Virginia},
Funding-Acknowledgement = {National Science Foundation (NSF) {[}1664061]},
Funding-Text = {<BOLD>Acknowledgements</BOLD> This work was supported by the National
   Science Foundation (NSF) under collaborative grant 1664061. We also
   thank and acknowledge the work of the larger HydroShare development team
   in this research. The authors would like to acknowledge the SWATShare
   team, especially Venkatesh Merwade and I Luk Kim, for their contribution
   in making SWATShare compatible with the SWAT MI content aggregations
   based on the new design of model aggregations presented in this paper.
   We also express our gratitude to two anonymous reviewers whose valuable
   comments contributed to the enhancement of this paper.},
Number-of-Cited-References = {36},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Environ. Modell. Softw.},
Doc-Delivery-Number = {DT4U4},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001134320700001},
DA = {2024-01-15},
}

@article{ WOS:000626563200001,
Author = {Boeing, Geoff},
Title = {Street Network Models and Indicators for Every Urban Area in the World},
Journal = {GEOGRAPHICAL ANALYSIS},
Year = {2022},
Volume = {54},
Number = {3, SI},
Pages = {519-535},
Month = {JUL},
Abstract = {Cities worldwide exhibit a variety of street network patterns and
   configurations that shape human mobility, equity, health, and
   livelihoods. This study models and analyzes the street networks of every
   urban area in the world, using boundaries derived from the Global Human
   Settlement Layer. Street network data are acquired and modeled from
   OpenStreetMap with the open-source OSMnx software. In total, this study
   models over 160 million OpenStreetMap street network nodes and over 320
   million edges across 8,914 urban areas in 178 countries, and attaches
   elevation and grade data. This article presents the study's reproducible
   computational workflow, introduces two new open data repositories of
   ready-to-use global street network models and calculated indicators, and
   discusses summary findings on street network form worldwide. It makes
   four contributions. First, it reports the methodological advances of
   this open-source workflow. Second, it produces an open data repository
   containing street network models for each urban area. Third, it analyzes
   these models to produce an open data repository containing street
   network form indicators for each urban area. No such global urban street
   network indicator data set has previously existed. Fourth, it presents a
   summary analysis of urban street network form, reporting the first such
   worldwide results in the literature.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Boeing, G (Corresponding Author), Univ Southern Calif, Dept Urban Planning \& Spatial Anal, Sol Price Sch Publ Policy, 301A Lewis Hall, Los Angeles, CA 90089 USA.
   Boeing, Geoff, Univ Southern Calif, Dept Urban Planning \& Spatial Anal, Sol Price Sch Publ Policy, 301A Lewis Hall, Los Angeles, CA 90089 USA.},
DOI = {10.1111/gean.12281},
EarlyAccessDate = {MAR 2021},
ISSN = {0016-7363},
EISSN = {1538-4632},
Keywords-Plus = {QUALITY ASSESSMENT; OPENSTREETMAP; INFORMATION},
Research-Areas = {Geography},
Web-of-Science-Categories  = {Geography},
Author-Email = {boeing@usc.edu},
Affiliations = {University of Southern California},
ResearcherID-Numbers = {Boeing, Geoff/P-3238-2019},
ORCID-Numbers = {Boeing, Geoff/0000-0003-1851-6411},
Funding-Acknowledgement = {Public Good Projects},
Funding-Text = {This work was funded in part by a grant from the Public Good Projects.},
Number-of-Cited-References = {49},
Times-Cited = {30},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {27},
Journal-ISO = {Geogr. Anal.},
Doc-Delivery-Number = {3F5ED},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000626563200001},
OA = {Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000381938600004,
Author = {Gomez, Nancy-Diana and Mendez, Eva and Hernandez-Perez, Tony},
Title = {SOCIAL SCIENCES AND HUMANITIES RESEARCH DATA AND METADATA: A PERSPECTIVE
   FROM THEMATIC DATA REPOSITORIES},
Journal = {PROFESIONAL DE LA INFORMACION},
Year = {2016},
Volume = {25},
Number = {4},
Pages = {545-555},
Month = {JUL-AUG},
Abstract = {This paper studies research data repositories in the social sciences and
   humanities (SSH), from the Registry of Research Data Repositories
   (re3data), paying particular attention to metadata models used to
   describe the datasets included in them. 397 repositories are reviewed at
   the general level, including those of a multidisciplinary nature. We
   discuss and reflect on the special features of research data in these
   disciplines, and on coverage and information collected by re3data. The
   metadata schemas and standards most commonly used in SSH repositories
   are analyzed, with special emphasis on the six main repositories.},
Publisher = {EPI},
Address = {APARTADO 32 280, BARCELONA, 08080, SPAIN},
Type = {Article},
Language = {English},
Affiliation = {Gómez, ND (Corresponding Author), Carlos III Univ Madrid UC3M, Arch \& Lib Digital Environm Program, Getafe, Madrid, Spain.
   Gomez, Nancy-Diana, Carlos III Univ Madrid UC3M, Arch \& Lib Digital Environm Program, Getafe, Madrid, Spain.
   Gomez, Nancy-Diana, UC3M, Dept Lib \& Informat Sci, Getafe, Madrid, Spain.
   Gomez, Nancy-Diana, Univ Buenos Aires, RA-1053 Buenos Aires, DF, Argentina.
   Gomez, Nancy-Diana, Univ Buenos Aires, Cent Lib, Fac Nat Sci, RA-1053 Buenos Aires, DF, Argentina.
   Mendez, Eva, Univ Carlos III Madrid, Dept Lib \& Informat Sci, E-28903 Getafe, Madrid, Spain.
   Hernandez-Perez, Tony, Univ Carlos III Madrid, Fac Humanidades Comunicac \& Documentac, C Madrid 128, E-28903 Getafe, Madrid, Spain.},
DOI = {10.3145/epi.2016.jul.04},
ISSN = {1386-6710},
Keywords = {Repositories; Research data; Metadata; Social sciences; Humanities;
   Re3data},
Research-Areas = {Communication; Information Science \& Library Science},
Web-of-Science-Categories  = {Communication; Information Science \& Library Science},
Author-Email = {ndgomez@bib.uc3m.es
   emendez@bib.uc3m.es
   tony@bib.uc3m.es},
Affiliations = {Universidad Carlos III de Madrid; University of Buenos Aires; University
   of Buenos Aires; Universidad Carlos III de Madrid; Universidad Carlos
   III de Madrid},
ResearcherID-Numbers = {Hernández-Pérez, Tony/K-7800-2013
   Méndez, Eva/A-6398-2010
   },
ORCID-Numbers = {Hernández-Pérez, Tony/0000-0001-8404-9247
   Méndez, Eva/0000-0002-5337-4722
   Gomez, Nancy Diana/0000-0002-6218-6248},
Funding-Acknowledgement = {Spanish State Program of Research, Development and Innovation Facing
   Society Challenges, Ministerio de Economia y Competitividad (Mineco),
   Spain {[}CSO2013-46754-R]},
Funding-Text = {This work is part of the project Curator-e: custody and digital
   management for the reuse of open data research in the humanities and
   social sciences, funded by the Spanish State Program of Research,
   Development and Innovation Facing Society Challenges, Ministerio de
   Economia y Competitividad (Mineco), Spain (CSO2013-46754-R).},
Number-of-Cited-References = {23},
Times-Cited = {14},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {62},
Journal-ISO = {Prof. Inf.},
Doc-Delivery-Number = {DU1AW},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000381938600004},
OA = {Bronze, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000396575500152,
Author = {Okuda, Shujiro and Watanabe, Yu and Moriya, Yuki and Kawano, Shin and
   Yamamoto, Tadashi and Matsumoto, Masaki and Takami, Tomoyo and
   Kobayashi, Daiki and Araki, Norie and Yoshizawa, Akiyasu C. and Tabata,
   Tsuyoshi and Sugiyama, Naoyuki and Goto, Susumu and Ishihama, Yasushi},
Title = {jPOSTrepo: an international standard data repository for proteomes},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2017},
Volume = {45},
Number = {D1},
Pages = {D1107-D1111},
Month = {JAN 4},
Abstract = {Major advancements have recently been made in mass spectrometry-based
   proteomics, yielding an increasing number of datasets from various
   proteomics projects worldwide. In order to facilitate the sharing and
   reuse of promising datasets, it is important to construct appropriate,
   high-quality public data repositories. jPOSTrepo
   (https://repository.jpostdb.org/) has successfully implemented several
   unique features, including high-speed file uploading, flexible file
   management and easy-to-use interfaces. This repository has been launched
   as a public repository containing various proteomic datasets and is
   available for researchers worldwide. In addition, our repository has
   joined the ProteomeXchange consortium, which includes the most popular
   public repositories such as PRIDE in Europe for MS/MS datasets and
   PASSEL for SRM datasets in the USA. Later MassIVE was introduced in the
   USA and accepted into the ProteomeXchange, as was our repository in July
   2016, providing important datasets from Asia/Oceania. Accordingly, this
   repository thus contributes to a global alliance to share and store all
   datasets from a wide variety of proteomics experiments. Thus, the
   repository is expected to become a major repository, particularly for
   data collected in the Asia/Oceania region.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Okuda, S (Corresponding Author), Niigata Univ, Grad Sch Med \& Dent Sci, Niigata 9518510, Japan.
   Ishihama, Y (Corresponding Author), Kyoto Univ, Grad Sch Pharmaceut Sci, Kyoto 6068501, Japan.
   Okuda, Shujiro; Watanabe, Yu; Ishihama, Yasushi, Niigata Univ, Grad Sch Med \& Dent Sci, Niigata 9518510, Japan.
   Moriya, Yuki; Kawano, Shin, Joint Support Ctr Data Sci Res, Database Ctr Life Sci, Res Org Informat \& Syst, Kashiwa, Chiba 2770871, Japan.
   Yamamoto, Tadashi, Niigata Univ, Biofluid Biomarker Ctr, Inst Social Innovat \& Cooperat, Niigata 9502181, Japan.
   Matsumoto, Masaki; Takami, Tomoyo, Kyushu Univ, Med Inst Bioregulat, Fukuoka 8128582, Japan.
   Kobayashi, Daiki; Araki, Norie, Kumamoto Univ, Grad Sch Med Sci, Fac Life Sci, Kumamoto 8608556, Japan.
   Yoshizawa, Akiyasu C.; Goto, Susumu, Kyoto Univ, Bioinformat Ctr, Inst Chem Res, Kyoto 6110011, Japan.
   Sugiyama, Naoyuki; Ishihama, Yasushi, Kyoto Univ, Grad Sch Pharmaceut Sci, Kyoto 6068501, Japan.},
DOI = {10.1093/nar/gkw1080},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MASS; IDENTIFICATION; UPDATE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {okd@med.niigata-u.ac.jp
   yishiham@pharm.kyoto-u.ac.jp},
Affiliations = {Niigata University; Research Organization of Information \& Systems
   (ROIS); Niigata University; Kyushu University; Kumamoto University;
   Kyoto University; Kyoto University},
ResearcherID-Numbers = {Yamamoto, Tadashi/IZE-7674-2023
   Sato, Miyuki/S-5112-2018
   Ishihama, Yasushi/B-3101-2016
   Okuda, Shujiro/D-1700-2016
   },
ORCID-Numbers = {Sato, Miyuki/0000-0002-1944-4918
   Ishihama, Yasushi/0000-0001-7714-203X
   Okuda, Shujiro/0000-0002-7704-8104
   Kawano, Shin/0000-0002-7969-2972
   Kobayashi, Daiki/0000-0003-4131-5220
   Matsumoto, Masaki/0000-0002-6987-0288
   Sugiyama, Naoyuki/0000-0001-7633-8495},
Funding-Acknowledgement = {National Bioscience Database Center, Japan Science and Technology Agency
   {[}15650519]; Grants-in-Aid for Scientific Research {[}16K07118,
   16K07198, 16K00416, 26242088] Funding Source: KAKEN},
Funding-Text = {Database Integration Coordination Program from National Bioscience
   Database Center, Japan Science and Technology Agency {[}15650519].
   Funding for open access charge: National Bioscience Database Center,
   Japan Science and Technology Agency {[}15650519].},
Number-of-Cited-References = {23},
Times-Cited = {334},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {EO3DQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000396575500152},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000622464200001,
Author = {Trisovic, Ana and Mika, Katherine and Boyd, Ceilyn and Feger, Sebastian
   and Crosas, Merce},
Title = {Repository Approaches to Improving the Quality of Shared Data and Code},
Journal = {DATA},
Year = {2021},
Volume = {6},
Number = {2},
Month = {FEB},
Abstract = {Sharing data and code for reuse has become increasingly important in
   scientific work over the past decade. However, in practice, shared data
   and code may be unusable, or published results obtained from them may be
   irreproducible. Data repository features and services contribute
   significantly to the quality, longevity, and reusability of datasets.
   This paper presents a combination of original and secondary data
   analysis studies focusing on computational reproducibility, data
   curation, and gamified design elements that can be employed to indicate
   and improve the quality of shared data and code. The findings of these
   studies are sorted into three approaches that can be valuable to data
   repositories, archives, and other research dissemination platforms.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Trisovic, A (Corresponding Author), Harvard Univ, Inst Quantitat Social Sci, 1737 Cambridge St, Cambridge, MA 02138 USA.
   Trisovic, Ana; Mika, Katherine; Boyd, Ceilyn; Crosas, Merce, Harvard Univ, Inst Quantitat Social Sci, 1737 Cambridge St, Cambridge, MA 02138 USA.
   Feger, Sebastian, European Org Nucl Res CERN, 1 Esplanade Particules, CH-1217 Meyrin, Switzerland.
   Feger, Sebastian, Ludwig Maximilians Univ Munchen, 1 Geschwister Scholl Pl, D-80539 Munich, Germany.},
DOI = {10.3390/data6020015},
Article-Number = {15},
EISSN = {2306-5729},
Keywords = {data quality; data repository; digital libraries; data curation; fair
   principles; open data; open code; gamification},
Keywords-Plus = {LONG TAIL},
Research-Areas = {Computer Science; Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Computer Science, Information Systems; Multidisciplinary Sciences},
Author-Email = {anatrisovic@g.harvard.edu
   kmika@g.harvard.edu
   boyd@harvard.edu
   sebastian.feger@ifi.lmu.de
   mcrosas@g.harvard.edu},
Affiliations = {Harvard University; University of Munich},
ORCID-Numbers = {Mika, Katherine/0000-0002-8839-0503
   Feger, Sebastian Stefan/0000-0002-0287-0945
   Boyd, Ceilyn/0000-0003-0044-232X},
Funding-Acknowledgement = {Sloan Foundation {[}G-2018-11111, P-2020-13988]; Council on Library and
   Information Resources (CLIR)},
Funding-Text = {This work is partially funded by the Sloan Foundation (award number
   G-2018-11111). Ana Trisovic is funded by the Sloan Foundation (award
   number P-2020-13988). Ana Trisovic acknowledges a micro-grant award by
   the Council on Library and Information Resources (CLIR). Sebastian Feger
   acknowledges CERN Doctoral Student program.},
Number-of-Cited-References = {43},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Data},
Doc-Delivery-Number = {QN4XL},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000622464200001},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000419550700138,
Author = {Song, Shuhui and Tian, Dongmei and Li, Cuiping and Tang, Bixia and Dong,
   Lili and Xiao, Jingfa and Bao, Yiming and Zhao, Wenming and He, Hang and
   Zhang, Zhang},
Title = {Genome Variation Map: a data repository of genome variations in BIG Data
   Center},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2018},
Volume = {46},
Number = {D1},
Pages = {D944-D949},
Month = {JAN 4},
Abstract = {The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public
   data repository of genome variations. As a core resource in the BIG Data
   Center, Beijing Institute of Genomics, Chinese Academy of Sciences, GVM
   dedicates to collect, integrate and visualize genome variations for a
   wide range of species, accepts submissions of different types of genome
   variations from all over the world and provides free open access to all
   publicly available data in support of worldwide research activities.
   Unlike existing related databases, GVM features integration of a large
   number of genome variations for a broad diversity of species including
   human, cultivated plants and domesticated animals. Specifically, the
   current implementation of GVM not only houses a total of similar to 4.9
   billion variants for 19 species including chicken, dog, goat, human,
   poplar, rice and tomato, but also incorporates 8669 individual genotypes
   and 13 262 manually curated high-quality genotype-to-phenotype
   associations for non-human species. In addition, GVM provides friendly
   intuitive web interfaces for data submission, browse, search and
   visualization. Collectively, GVM serves as an important resource for
   archiving genomic variation data, helpful for better understanding
   population genetic diversity and deciphering complex mechanisms
   associated with different phenotypes.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Song, SH; Zhang, Z (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Zhang, Z (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Z (Corresponding Author), Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Zhang, Z (Corresponding Author), Fudan Univ, Collaborat Innovat Ctr Genet \& Dev, Shanghai 200438, Peoples R China.
   Song, Shuhui; Tian, Dongmei; Li, Cuiping; Tang, Bixia; Dong, Lili; Xiao, Jingfa; Bao, Yiming; Zhao, Wenming; Zhang, Zhang, Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Tang, Bixia; Xiao, Jingfa; Bao, Yiming; Zhang, Zhang, Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Tang, Bixia; Xiao, Jingfa; Zhang, Zhang, Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Xiao, Jingfa; Zhang, Zhang, Fudan Univ, Collaborat Innovat Ctr Genet \& Dev, Shanghai 200438, Peoples R China.
   He, Hang, Peking Univ, Sch Life Sci, Beijing 100871, Peoples R China.},
DOI = {10.1093/nar/gkx986},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {ARCHIVE; GROWTH},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {songshh@big.ac.cn
   zhangzhang@big.ac.cn},
Affiliations = {Chinese Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese
   Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese Academy
   of Sciences; University of Chinese Academy of Sciences, CAS; Fudan
   University; Peking University},
ResearcherID-Numbers = {zhang, zhang/GQZ-6804-2022
   zhang, zheng/HCH-9684-2022
   song, shuhui/D-6015-2014
   He, Hang/ABF-4074-2020
   tian, dongmei/HIR-8892-2022
   xiao, jing/HRB-7391-2023
   Zhang, Zhang/JAX-2097-2023
   },
ORCID-Numbers = {tian, dongmei/0000-0003-0564-625X
   He, Hang/0000-0003-3165-283X
   Zhang, Zhang/0000-0001-6603-5060},
Funding-Acknowledgement = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDB13040500, XDA08020102]; National Key Research \& Development
   Program of China {[}2016YFE0206600, 2017YFC0907502]; National Key
   Research Program of China {[}2016YFC0901603, 2016YFB0201702,
   2016YFC0901903]; National Programs for High Technology Research and
   Development {[}863 Program] {[}2015AA020108]; Youth Innovation Promotion
   Association of Chinese Academy of Science {[}2017141]; National Natural
   Science Foundation of China {[}30900831]; International Partnership
   Program of the Chinese Academy of Sciences {[}153F11KYSB20160008]; Key
   Program of the Chinese Academy of Sciences {[}KJZD-EW-L14]; Key
   Technology Talent Program of the Chinese Academy of Sciences; 100 Talent
   Program of the Chinese Academy of Sciences; Strategic Priority Research
   Program of the Chinese Academy of Sciences},
Funding-Text = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDB13040500 to Z.Z., W.Z.; XDA08020102 to Z.Z.]; National Key
   Research \& Development Program of China {[}2016YFE0206600 to Y.B.;
   2017YFC0907502 to Z.Z.]; National Key Research Program of China
   {[}2016YFC0901603 to W.Z.; 2016YFB0201702, 2016YFC0901903 to J.X.];
   National Programs for High Technology Research and Development {[}863
   Program; 2015AA020108 to Z.Z.]; The Youth Innovation Promotion
   Association of Chinese Academy of Science {[}2017141 to S.S.]; National
   Natural Science Foundation of China {[}30900831 to S.S.]; International
   Partnership Program of the Chinese Academy of Sciences
   {[}153F11KYSB20160008]; Key Program of the Chinese Academy of Sciences
   {[}KJZD-EW-L14 to J.X.]; Key Technology Talent Program of the Chinese
   Academy of Sciences (to W.Z.); The 100 Talent Program of the Chinese
   Academy of Sciences (to Y.B. and Z.Z.). Funding for open access charge:
   Strategic Priority Research Program of the Chinese Academy of Sciences.},
Number-of-Cited-References = {22},
Times-Cited = {41},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {20},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {FS1QA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000419550700138},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000429427900007,
Author = {Nargesian, Fatemeh and Zhu, Erkang and Pu, Ken Q. and Miller, Renee J.},
Title = {Table Union Search on Open Data},
Journal = {PROCEEDINGS OF THE VLDB ENDOWMENT},
Year = {2018},
Volume = {11},
Number = {7},
Pages = {813-825},
Month = {MAR},
Abstract = {We define the table union search problem and present a probabilistic
   solution for finding tables that are unionable with a query table within
   massive repositories. Two tables are unionable if they share attributes
   from the same domain. Our solution formalizes three statistical models
   that describe how unionable attributes are generated from set domains,
   semantic domains with values from an ontology, and natural language
   domains. We propose a data-driven approach that automatically determines
   the best model to use for each pair of attributes. Through a
   distribution-aware algorithm, we are able to find the optimal number of
   attributes in two tables that can be unioned. To evaluate accuracy, we
   created and open-sourced a benchmark of Open Data tables. We show that
   our table union search outperforms in speed and accuracy existing
   algorithms for finding related tables and scales to provide efficient
   search over Open Data repositories containing more than one million
   attributes.},
Publisher = {ASSOC COMPUTING MACHINERY},
Address = {1601 Broadway, 10th Floor, NEW YORK, NY USA},
Type = {Article},
Language = {English},
Affiliation = {Nargesian, F (Corresponding Author), Univ Toronto, Toronto, ON, Canada.
   Nargesian, Fatemeh; Zhu, Erkang; Miller, Renee J., Univ Toronto, Toronto, ON, Canada.
   Pu, Ken Q., UOIT, Oshawa, ON, Canada.},
DOI = {10.14778/3192965.3192973},
ISSN = {2150-8097},
Keywords-Plus = {SCALE},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Computer Science, Theory \&
   Methods},
Author-Email = {fnargesian@cs.toronto.edu
   ekzhu@cs.toronto.edu
   ken.pu@uoit.ca
   miller@cs.toronto.edu},
Affiliations = {University of Toronto; Ontario Tech University},
ORCID-Numbers = {Nargesian, Fatemeh/0000-0002-4710-8719},
Funding-Acknowledgement = {NSERC},
Funding-Text = {This work was partially supported by NSERC.},
Number-of-Cited-References = {39},
Times-Cited = {71},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Proc. VLDB Endow.},
Doc-Delivery-Number = {GB9XK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000429427900007},
DA = {2024-01-15},
}

@article{ WOS:000571460000001,
Author = {Falconi, Nereyda and Fuller, Todd K. and DeStefano, Stephen and Organ,
   John F.},
Title = {An open-access occurrence database for Andean bears in Peru},
Journal = {URSUS},
Year = {2020},
Volume = {31},
Number = {E11},
Month = {JAN},
Abstract = {The Andean bear (Tremarctos ornatus) is listed as a vulnerable species
   by the International Union for Conservation of Nature; however, the lack
   of knowledge regarding different aspects of its ecology, biogeography,
   and abundance hinders the conservation efforts of researchers and
   managers. To address the high cost of acquiring information and the lack
   of systematized data, we created a database for records of this species
   in Peru. We compiled Andean bear occurrence records in Peru for the
   years 1980-2018 from different sources, including direct observations,
   indirect observations (footprints, food remains, bear beds and scats),
   and camera-trap photographs from published literature, gray literature,
   and environmental impact studies. With collaboration from many
   colleagues, we obtained 973 records and created an open access database
   by using the Global Biodiversity Information Facility data repository.
   We encourage the use, publication, and sharing of raw data from studies
   and opportunistic observations to gain better knowledge and support for
   the conservation of the Andean bear and other threatened species.},
Publisher = {INT ASSOC BEAR RESEARCH \& MANAGEMENT-IBA},
Address = {C/O TERRY WHITE, UNIV TENNESSEE, DEPT FORESTRY, WILDLIFE \& FISHERIES,
   PO BOX 1071, KNOXVILLE, TN 37901-1071 USA},
Type = {Article},
Language = {English},
Affiliation = {Falconi, N (Corresponding Author), Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
   Falconi, N (Corresponding Author), Univ Massachusetts, Massachusetts Cooperat Fish \& Wildlife Res Unit, Amherst, MA 01003 USA.
   Falconi, Nereyda; Fuller, Todd K., Univ Massachusetts, Dept Environm Conservat, Amherst, MA 01003 USA.
   DeStefano, Stephen, Univ Massachusetts, Massachusetts Cooperat Fish \& Wildlife Res Unit, US Geol Survey, Amherst, MA 01003 USA.
   Organ, John F., US Geol Survey, Cooperat Res Units Program, Reston, VA 20192 USA.
   Falconi, Nereyda, Univ Massachusetts, Massachusetts Cooperat Fish \& Wildlife Res Unit, Amherst, MA 01003 USA.},
DOI = {10.2192/URSUS-D-19-00012.1},
Article-Number = {e11},
ISSN = {1537-6176},
EISSN = {1938-5439},
Keywords = {Andean bear; data availability; distribution; occurrence; oso andino;
   oso de anteojos; spectacled bear; Tremarctos ornatus},
Research-Areas = {Zoology},
Web-of-Science-Categories  = {Zoology},
Author-Email = {nfalconilope@umass.edu},
Affiliations = {University of Massachusetts System; University of Massachusetts Amherst;
   University of Massachusetts System; University of Massachusetts Amherst;
   United States Department of the Interior; United States Geological
   Survey; United States Department of the Interior; United States
   Geological Survey; University of Massachusetts System; University of
   Massachusetts Amherst},
Funding-Acknowledgement = {International Bear Association; Wildlife Conservation Society},
Funding-Text = {We thank the International Bear Association for their support via a
   Research and Conservation Grant, and the Wildlife Conservation Society
   for a Christensen Conservation Leaders Scholarship to NF. Thanks to
   everyone who shared their data and special thanks to J. Amanzo, R.
   VanHorn, and R. Wallace for their help. Special thanks to D. Wattles for
   his review of this manuscript, which greatly improved the content. Any
   use of trade, firm, or product names is for descriptive purposes only
   and does not imply endorsement by the U.S. Government.},
Number-of-Cited-References = {13},
Times-Cited = {5},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Ursus},
Doc-Delivery-Number = {NR3JY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000571460000001},
DA = {2024-01-15},
}

@article{ WOS:000366151000016,
Author = {Tardif, Christine Lucas and Schaefer, Andreas and Trampel, Robert and
   Villringer, Arno and Turner, Robert and Bazin, Pierre-Louis},
Title = {Open Science CBS Neuroimaging Repository: Sharing ultra-high-field MR
   images of the brain},
Journal = {NEUROIMAGE},
Year = {2016},
Volume = {124},
Number = {B, SI},
Pages = {1143-1148},
Month = {JAN 1},
Abstract = {Magnetic resonance imaging at ultra high field opens the door to
   quantitative brain imaging at sub-millimeter isotropic resolutions.
   However, novel image processing tools to analyze these new rich datasets
   are lacking. In this article, we introduce the Open Science CBS
   Neuroimaging Repository: a unique repository of high-resolution and
   quantitative images acquired at 7 T. The motivation for this project is
   to increase interest for high-resolution and quantitative imaging and
   stimulate the development of image processing tools developed
   specifically for high-field data. Our growing repository currently
   includes datasets from MP2RAGE and multi-echo FLASH sequences from 28
   and 20 healthy subjects respectively. These datasets represent the
   current state-of-the-art in in-vivo relaxometry at 7 T, and are now
   fully available to the entire neuroimaging community. (C) 2015 Elsevier
   Inc. All rights reserved.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Tardif, CL (Corresponding Author), Max Planck Inst Human Cognit \& Brain Sci, Stephanstr 1A, D-04103 Leipzig, Germany.
   Tardif, Christine Lucas; Villringer, Arno; Bazin, Pierre-Louis, Max Planck Inst Human Cognit \& Brain Sci, Dept Neurol, D-04103 Leipzig, Germany.
   Schaefer, Andreas; Trampel, Robert; Turner, Robert, Max Planck Inst Human Cognit \& Brain Sci, Dept Neurophys, D-04103 Leipzig, Germany.},
DOI = {10.1016/j.neuroimage.2015.08.042},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords = {Data repository; Ultra-high field; Magnetic resonance imaging;
   Quantitative imaging; High-resolution imaging; Relaxometry},
Keywords-Plus = {SUSCEPTIBILITY MAPPING QSM; VOXEL-BASED-MORPHOMETRY; IN-VIVO; 7 T;
   MAGNETIC-RESONANCE; CEREBRAL-CORTEX; GRAY-MATTER; T-1; CONTRAST;
   REGISTRATION},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {ctardif@cbs.mpg.de},
Affiliations = {Max Planck Society; Max Planck Society},
ResearcherID-Numbers = {Schäfer, Andreas/I-6014-2014
   },
ORCID-Numbers = {Schäfer, Andreas/0000-0001-5753-1839
   Turner, Robert/0000-0001-5055-9644
   Villringer, Arno/0000-0003-2604-2404
   Bazin, Pierre-Louis/0000-0002-0141-5510},
Number-of-Cited-References = {64},
Times-Cited = {15},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {CY1FB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000366151000016},
DA = {2024-01-15},
}

@article{ WOS:000462587400165,
Author = {Moriya, Yuki and Kawano, Shin and Okuda, Shujiro and Watanabe, Yu and
   Matsumoto, Masaki and Takami, Tomoyo and Kobayashi, Daiki and
   Yamanouchi, Yoshinori and Araki, Norie and Yoshizawa, Akiyasu C. and
   Tabata, Tsuyoshi and Iwasaki, Mio and Sugiyama, Naoyuki and Tanaka,
   Satoshi and Goto, Susumu and Ishihama, Yasushi},
Title = {The jPOST environment: an integrated proteomics data repository and
   database},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2019},
Volume = {47},
Number = {D1},
Pages = {D1218-D1224},
Month = {JAN 8},
Abstract = {Rapid progress is being made in mass spectrometry (MS)-based proteomics,
   yielding an increasing number of larger datasets with higher quality and
   higher throughput. To integrate proteomics datasets generated from
   various projects and institutions, we launched a project named jPOST
   (Japan ProteOme STandard Repository/Database, https://jpostdb.org/) in
   2015. Its proteomics data repository, jPOSTrepo, began operations in
   2016 and has accepted more than 10 TB of MS-based proteomics datasets in
   the past two years. In addition, we have developed a new proteomics
   database named jPOSTdb in which the published raw datasets in jPOSTrepo
   are reanalyzed using standardized protocol. jPOSTdb provides viewers
   showing the frequency of detected post-translational modifications, the
   co-occurrence of phosphorylation sites on a peptide and peptide sharing
   among proteoforms. jPOSTdb also provides basic statistical analysis
   tools to compare proteomics datasets.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Goto, S (Corresponding Author), Res Org Informat \& Syst, Database Ctr Life Sci, Joint Support Ctr Data Sci Res, Kashiwa, Chiba 2770871, Japan.
   Ishihama, Y (Corresponding Author), Kyoto Univ, Grad Sch Pharmaceut Sci, Kyoto 6068501, Japan.
   Moriya, Yuki; Kawano, Shin; Goto, Susumu, Res Org Informat \& Syst, Database Ctr Life Sci, Joint Support Ctr Data Sci Res, Kashiwa, Chiba 2770871, Japan.
   Okuda, Shujiro; Watanabe, Yu, Niigata Univ, Grad Sch Med \& Dent Sci, Niigata 3518510, Japan.
   Matsumoto, Masaki; Takami, Tomoyo, Kyushu Univ, Med Inst Bioregulat, Fukuoka, Fukuoka 8128582, Japan.
   Kobayashi, Daiki; Yamanouchi, Yoshinori; Araki, Norie, Kumamoto Univ, Grad Sch Med Sci, Fac Life Sci, Kumamoto 8608556, Japan.
   Yamanouchi, Yoshinori, Kumamoto Univ Hosp, Kumamoto 8608556, Japan.
   Yoshizawa, Akiyasu C.; Tabata, Tsuyoshi; Sugiyama, Naoyuki; Ishihama, Yasushi, Kyoto Univ, Grad Sch Pharmaceut Sci, Kyoto 6068501, Japan.
   Tabata, Tsuyoshi; Iwasaki, Mio, Kyoto Univ, Ctr iPS Cell Res \& Applicat, Kyoto 6068507, Japan.
   Tanaka, Satoshi, Trans IT, Kaminokawa 3290607, Japan.},
DOI = {10.1093/nar/gky899},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {ONTOLOGY; CONSORTIUM; NEXTPROT; DISEASES; PROTEIN; UPDATE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {goto@dbcls.rois.ac.jp
   yishihama@pharm.kyoto-u.ac.jp},
Affiliations = {Research Organization of Information \& Systems (ROIS); Niigata
   University; Kyushu University; Kumamoto University; Kumamoto University;
   Kyoto University; Kyoto University},
ResearcherID-Numbers = {Ishihama, Yasushi/B-3101-2016
   Okuda, Shujiro/D-1700-2016
   },
ORCID-Numbers = {Ishihama, Yasushi/0000-0001-7714-203X
   Okuda, Shujiro/0000-0002-7704-8104
   Sugiyama, Naoyuki/0000-0001-7633-8495
   Kobayashi, Daiki/0000-0003-4131-5220
   Iwasaki, Mio/0000-0003-2085-732X
   Matsumoto, Masaki/0000-0002-6987-0288},
Funding-Acknowledgement = {National Bioscience Database Center, Japan Science and Technology Agency
   {[}15650519, 18063028]},
Funding-Text = {Database Integration Coordination Program from National Bioscience
   Database Center, Japan Science and Technology Agency {[}15650519,
   18063028]. Funding for open access charge: National Bioscience Database
   Center, Japan Science and Technology Agency {[}18063028].},
Number-of-Cited-References = {31},
Times-Cited = {66},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {HQ7GH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000462587400165},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000556939800001,
Author = {Nishikawa, Kai},
Title = {How are research data governed at Japanese repositories? A knowledge
   commons perspective},
Journal = {ASLIB JOURNAL OF INFORMATION MANAGEMENT},
Year = {2020},
Volume = {72},
Number = {5},
Pages = {837-852},
Month = {SEP 21},
Abstract = {Purpose The purpose of this paper is to survey how research data are
   governed at repositories in Japan by deductively establishing a
   governance typology based on the concept of openness in the context of
   knowledge commons and empirically assessing the conformity of
   repositories to each type. Design/methodology/approach The fuzzy-set
   ideal type analysis (FSITA) was adopted. For data collection, a manual
   assessment was conducted with all Japanese research data repositories
   registered on re3data.org. Findings The typology constructed in this
   paper consists of three dimensions: openness to resources (here equal to
   research data), openness to a community and openness to infrastructure
   provision. This paper found that there is no case where all dimensions
   are open, and there are several cases where the resources are closed
   despite research data repositories being positioned as a basis for open
   science in Japanese science and technology policy. Originality/value
   This is likely the first construction of the typology and application of
   FSITA to the study of research data governance based on knowledge
   commons. The findings of this paper provide practitioners insight into
   how to govern research data at repositories. The typology serves as a
   first step for future research on knowledge commons, for example, as a
   criterion of case selection in conducting in-depth case studies.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Nishikawa, K (Corresponding Author), Univ Tsukuba, Grad Sch Lib Informat \& Media Studies, Tsukuba, Ibaraki, Japan.
   Nishikawa, Kai, Univ Tsukuba, Grad Sch Lib Informat \& Media Studies, Tsukuba, Ibaraki, Japan.},
DOI = {10.1108/AJIM-03-2020-0072},
EarlyAccessDate = {JUL 2020},
ISSN = {2050-3806},
EISSN = {1758-3748},
Keywords = {Research data; Open science; Data governance; Fuzzy-set ideal type
   analysis; Knowledge commons; Research data repository},
Keywords-Plus = {IDEAL TYPE ANALYSIS; TYPOLOGY; WELFARE},
Research-Areas = {Computer Science; Information Science \& Library Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Information Science \& Library
   Science},
Author-Email = {kai.nishikawa192000@gmail.com},
Affiliations = {University of Tsukuba},
ORCID-Numbers = {Nishikawa, Kai/0000-0001-5949-3610},
Number-of-Cited-References = {51},
Times-Cited = {1},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {35},
Journal-ISO = {Aslib J. Inf. Manag.},
Doc-Delivery-Number = {PB2HK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000556939800001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000426155900001,
Author = {Bhattacharya, Sanchita and Dunn, Patrick and Thomas, Cristel G. and
   Smith, Barry and Schaefer, Henry and Chen, Jieming and Hu, Zicheng and
   Zalocusky, Kelly A. and Shankar, Ravi D. and Shen-Orr, Shai S. and
   Thomson, Elizabeth and Wiser, Jeffrey and Butte, Atul J.},
Title = {ImmPort, toward repurposing of open access immunological assay data for
   translational and clinical research},
Journal = {SCIENTIFIC DATA},
Year = {2018},
Volume = {5},
Month = {FEB 27},
Abstract = {Immunology researchers are beginning to explore the possibilities of
   reproducibility, reuse and secondary analyses of immunology data.
   Open-access datasets are being applied in the validation of the methods
   used in the original studies, leveraging studies for meta-analysis, or
   generating new hypotheses. To promote these goals, the ImmPort data
   repository was created for the broader research community to explore the
   wide spectrum of clinical and basic research data and associated
   findings. The ImmPort ecosystem consists of four components-Private
   Data, Shared Data, Data Analysis, and Resources-for data archiving,
   dissemination, analyses, and reuse. To date, more than 300 studies have
   been made freely available through the Shared Data portal (immport.
   org/immportopen), which allows research data to be repurposed to
   accelerate the translation of new insights into discoveries.},
Publisher = {NATURE PUBLISHING GROUP},
Address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bhattacharya, S (Corresponding Author), Univ Calif San Francisco, Inst Computat Hlth Sci, San Francisco, CA 94158 USA.
   Bhattacharya, Sanchita; Chen, Jieming; Hu, Zicheng; Zalocusky, Kelly A.; Butte, Atul J., Univ Calif San Francisco, Inst Computat Hlth Sci, San Francisco, CA 94158 USA.
   Dunn, Patrick; Thomas, Cristel G.; Thomson, Elizabeth; Wiser, Jeffrey, Northrop Grumman Hlth Solut, Rockville, MD 20850 USA.
   Smith, Barry, Univ Buffalo, Dept Philosophy, Buffalo, NY 14260 USA.
   Schaefer, Henry, Enterprise Sci \& Comp Inc, Rockville, MD 20850 USA.
   Shankar, Ravi D., Stanford Univ, Dept Med, Sch Med, Stanford, CA 94305 USA.
   Shen-Orr, Shai S., Technion Israel Inst Technol, Dept Immunol, Fac Med, IL-3200003 Haifa, Israel.},
DOI = {10.1038/sdata.2018.15},
Article-Number = {180015},
EISSN = {2052-4463},
Keywords-Plus = {PROTEIN ONTOLOGY; CYTOMETRY DATA; TRIAL DATA; REPRESENTATION; ENTITIES;
   SUBSETS; NETWORK; VACCINE},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {Sanchita.Bhattacharya@ucsf.edu},
Affiliations = {University of California System; University of California San Francisco;
   State University of New York (SUNY) System; State University of New York
   (SUNY) Buffalo; Stanford University; Technion Israel Institute of
   Technology},
ResearcherID-Numbers = {Shankar, Ravi/HSF-1169-2023
   Smith, Barry/A-9525-2011
   },
ORCID-Numbers = {Smith, Barry/0000-0003-1384-116X
   Dunn, Patrick/0000-0003-1868-9689
   Bhattacharya, Sanchita/0000-0002-3056-0733
   Schaefer, Henry/0000-0002-3492-811X
   Shen-Orr, Shai/0000-0002-6991-7736
   Thomas, Cristel/0000-0001-8310-9666},
Funding-Acknowledgement = {National Institute of Allergy and Infectious Diseases
   {[}HHSN272201200028C]; National Institute for General Medical Science
   {[}R01GM080646]},
Funding-Text = {This work was supported by the National Institute of Allergy and
   Infectious Diseases (Bioinformatics Support Contract HHSN272201200028C)
   and by the National Institute for General Medical Science (R01GM080646).
   The authors thank Quan Chen, Gabriel Rosenfeld, Dawei Lin at the
   National Institute of Allergy and Infectious Diseases for their
   oversight of the program. The ImmPort project is brought to fruition by
   the development team including Patricia Berger, John Campbell, Srinivas
   Chepuri, Vincent Desborough, Patricia Guimaraes, Ruth Montero, Thomas
   Smith, and Bryan Walters. The interactions with the HIPC Standards
   Working Group (Kei-Hoi Cheung, Alexander Diehl, Steven Kleinstein,
   Subhasis Mohanty, Bjoern Peters, Randi Vita) are invaluable. We also
   thank Theodore Goldstein for his valuable input during the manuscript
   preparation. The content is solely the responsibility of the authors and
   does not necessarily represent the official views of the National
   Institutes of Health. The funders had no role in study design, data
   collection and analysis, decision to publish, or preparation of the
   manuscript. The paper was written by S.B. and P.D. with editorial input
   from B.S. and all the other coauthors. C.T., H.S., E.T., and P.D. are
   responsible for data capture and curation. T.S., J.C., V.D. and P.D.
   design the data model. T.S. implements the data upload software. P.B.,
   J.C., S.C., P.G., and R.M. build and test the software. ET and JW are
   current and former project managers. T.S., K.Z., J.C., Z.H., R.S., S.S.
   and S.B. conducted the data repurposing projects. A.B. provided feedback
   regarding design, analysis and implementation throughout the data
   repurposing and manuscript generation projects.},
Number-of-Cited-References = {27},
Times-Cited = {410},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Sci. Data},
Doc-Delivery-Number = {FX5XM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000426155900001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000650047300007,
Author = {Gilyarevskii, R. S. and Mel'nikova, V, E.},
Title = {The Peculiarities of Data Access within the Information Infrastructure
   of Modern Science},
Journal = {SCIENTIFIC AND TECHNICAL INFORMATION PROCESSING},
Year = {2021},
Volume = {48},
Number = {1},
Pages = {53-57},
Month = {JAN},
Abstract = {Brief characteristics of the information infrastructure of modern
   science are presented and its definition is given. The issue of
   scientific data management, the ensuring of the full life cycle of data
   is considered in detail. The main points of the Scientific Data
   Management Plan identified by the expert community are given. Special
   attention is given in the Plan to the points concerning the conditions
   of user access to the results of scientific research and the volumes in
   which the final data is supposed to be presented to the scientific
   community. The order and main objectives of the meta-description of
   scientific data are outlined; the important role of unique global
   identifiers is noted. The content of the Fair Data Principles concept in
   the understanding of Harvard University and the European Commission on
   Research and Innovation is revealed. The detailed characteristics of a
   fundamentally new digital open access resource, the Register of
   Scientific Data Repositories Re3Data.org are given. The role of the
   Register as an important tool of open science is emphasized. Using the
   example of the American HatiTrust repository library, a form of
   semi-closed access to data is presented. The existence of semi-closed
   access in parallel with open access is noted. The specificities of
   access to data in modern science magazines are reflected. The importance
   of the development of an appropriate legal framework to regulate the
   ability to use various types of access to scientific data is formulated.},
Publisher = {ALLERTON PRESS INC},
Address = {18 WEST 27TH ST, NEW YORK, NY 10001 USA},
Type = {Article},
Language = {English},
Affiliation = {Gilyarevskii, RS (Corresponding Author), Russian Acad Sci, All Russian Inst Sci \& Tech Informat VINITI, Moscow 125315, Russia.
   Gilyarevskii, RS (Corresponding Author), Lomonosov Moscow State Univ, Fac Journalism, Moscow 125009, Russia.
   Gilyarevskii, R. S.; Mel'nikova, E., V, Russian Acad Sci, All Russian Inst Sci \& Tech Informat VINITI, Moscow 125315, Russia.
   Gilyarevskii, R. S., Lomonosov Moscow State Univ, Fac Journalism, Moscow 125009, Russia.},
DOI = {10.3103/S0147688221010111},
ISSN = {0147-6882},
EISSN = {1934-8118},
Keywords = {information infrastructure of science; scientific data management; open
   science; open access; FAIR Data Principles concept; scientific
   repositories; Register of scientific repositories; science magazines;
   science publishers},
Keywords-Plus = {LIBRARIES},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {giliarevski@viniti.ru
   verden.mel@yandex.ru},
Affiliations = {Russian Academy of Sciences; Institute for Scientific \& Technical
   Information of the Russian Academy of Sciences; Lomonosov Moscow State
   University},
Funding-Acknowledgement = {state task of VINITI RAS {[}0003-2019-0001]; Russian Foundation for
   Basic Research {[}20-07-00014]},
Funding-Text = {This study was carried out under the state task of VINITI RAS (topic no.
   0003-2019-0001) and with the support of the Russian Foundation for Basic
   Research (project no. 20-07-00014).},
Number-of-Cited-References = {11},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Sci. Tech. Inf. Process.},
Doc-Delivery-Number = {SB5QA},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000650047300007},
DA = {2024-01-15},
}

@article{ WOS:000396783900006,
Author = {Landsiedel, Christian and Wollherr, Dirk},
Title = {Road geometry estimation for urban semantic maps using open data},
Journal = {ADVANCED ROBOTICS},
Year = {2017},
Volume = {31},
Number = {5},
Pages = {282-290},
Abstract = {Complex robotic tasks require the use of knowledge that cannot be
   acquired with the sensor repertoire of a mobile, autonomous robot alone.
   For robots navigating in urban environments, geospatial open data
   repositories such as OpenStreetMap (OSM) provide a source for such
   knowledge. We propose the integration of a 3D metric environment
   representation with the semantic knowledge from such a database. The
   application we describe uses street network information from OSM to
   improve street geometry information determined from laser data. This
   approach is evaluated on a challenging data-set of the Munich inner
   city.},
Publisher = {TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Landsiedel, C (Corresponding Author), Tech Univ Munich, Inst Automat Control Engn LSR, Munich, Germany.
   Landsiedel, Christian; Wollherr, Dirk, Tech Univ Munich, Inst Automat Control Engn LSR, Munich, Germany.},
DOI = {10.1080/01691864.2016.1250675},
ISSN = {0169-1864},
EISSN = {1568-5535},
Keywords = {Spatial reasoning; hybrid maps; scene understanding},
Keywords-Plus = {OPENSTREETMAP},
Research-Areas = {Robotics},
Web-of-Science-Categories  = {Robotics},
Author-Email = {christian.landsiedel@tum.de},
Affiliations = {Technical University of Munich},
ResearcherID-Numbers = {Wollherr, Dirk/C-3925-2011},
ORCID-Numbers = {Wollherr, Dirk/0000-0003-2810-6790},
Number-of-Cited-References = {19},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Adv. Robot.},
Doc-Delivery-Number = {EO6EE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000396783900006},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000753496500001,
Author = {Jwa, Anita S. and Poldrack, Russell A.},
Title = {The spectrum of data sharing policies in neuroimaging data repositories},
Journal = {HUMAN BRAIN MAPPING},
Year = {2022},
Volume = {43},
Number = {8},
Pages = {2707-2721},
Month = {JUN 1},
Abstract = {Sharing data is a scientific imperative that accelerates scientific
   discoveries, reinforces open science inquiry, and allows for efficient
   use of public investment and research resources. Considering these
   benefits, data sharing has been widely promoted in diverse fields and
   neuroscience has been no exception to this movement. For all its
   promise, however, the sharing of human neuroimaging data raises critical
   ethical and legal issues, such as data privacy. Recently, the heightened
   risks to data privacy posed by the rapid advances in artificial
   intelligence and machine learning techniques have made data sharing more
   challenging; the regulatory landscape around data sharing has also been
   evolving rapidly. Here we present an in-depth ethical and regulatory
   analysis that examines how neuroimaging data are currently shared
   against the backdrop of the relevant regulations and policies in the
   United States and how advanced software tools and algorithms might
   undermine subjects' privacy in neuroimaging data sharing. The
   implications of these novel technological threats to privacy in
   neuroimaging data sharing practices and policies will also be discussed.
   We then conclude with a proposal for a legal prohibition against
   malicious use of neuroscience data as a regulatory mechanism to address
   privacy risks associated with the data while maximizing the benefits of
   data sharing and open science practice in the field of neuroscience.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Review},
Language = {English},
Affiliation = {Jwa, AS (Corresponding Author), Stanford Univ, Dept Psychol, 450 Jane Stanford Way,Bldg 420, Stanford, CA 94305 USA.
   Jwa, Anita S.; Poldrack, Russell A., Stanford Univ, Dept Psychol, 450 Jane Stanford Way,Bldg 420, Stanford, CA 94305 USA.},
DOI = {10.1002/hbm.25803},
EarlyAccessDate = {FEB 2022},
ISSN = {1065-9471},
EISSN = {1097-0193},
Keywords = {data privacy; data re-identification; data sharing; data use agreement;
   neuroethics; neuroimaging},
Keywords-Plus = {INDIVIDUAL-DIFFERENCES; DEIDENTIFICATION; DISEASE},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {anniejwa@stanford.edu},
Affiliations = {Stanford University},
ORCID-Numbers = {Jwa, Anita/0000-0002-1462-424X},
Funding-Acknowledgement = {National Institute of Mental Health (NIMH) {[}3R24MH117179-03S1]},
Funding-Text = {This article was fully funded by the National Institute of Mental Health
   (NIMH) grant number 3R24MH117179-03S1.},
Number-of-Cited-References = {66},
Times-Cited = {15},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Hum. Brain Mapp.},
Doc-Delivery-Number = {1N5QM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000753496500001},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:001015209000001,
Author = {Nguyen, Tran B. and Bates, Kelvin H. and Buenconsejo, Reina S. and
   Charan, Sophia M. and Cavanna, Eric E. and Cocker III, David R. and Day,
   Douglas A. and DeVault, Marla P. and Donahue, Neil M. and Finewax,
   Zachary and Habib, Luke F. and Handschy, Anne V. and Ruiz, Lea
   Hildebrandt and Hou, Chung-Yi S. and Jimenez, Jose L. and Joo, Taekyu
   and Klodt, Alexandra L. and Kong, Weimeng and Le, Chen and Masoud,
   Catherine G. and Mayernik, Matthew S. and Ng, Nga L. and Nienhouse, Eric
   J. and Nizkorodov, Sergey A. and Orlando, John J. and Post, Jeroen J.
   and Sturm, Patrick O. and Thrasher, Bridget L. and Tyndall, Geoffrey S.
   and Seinfeld, John H. and Worley, Steven J. and Zhang, Xuan and Ziemann,
   Paul J.},
Title = {Overview of ICARUS-A Curated, Open Access, Online Repository for
   Atmospheric Simulation Chamber Data},
Journal = {ACS EARTH AND SPACE CHEMISTRY},
Year = {2023},
Volume = {7},
Number = {6},
Pages = {1235-1246},
Month = {MAY 16},
Abstract = {Atmospheric simulationchambers continue to be indispensable toolsfor
   research in the atmospheric sciences. Insights from chamber studiesare
   integrated into atmospheric chemical transport models, which areused for
   science-informed policy decisions. However, a centralizeddata management
   and access infrastructure for their scientific productshad not been
   available in the United States and many parts of theworld. ICARUS
   (Integrated Chamber Atmospheric data Repository forUnified Science) is
   an open access, searchable, web-based infrastructurefor storing,
   sharing, discovering, and utilizing atmospheric chamberdata
   {[}https://icarus.ucdavis.edu]. ICARUS has two parts: a data intake
   portal and a search and discoveryportal. Data in ICARUS are curated,
   uniform, interactive, indexedon popular search engines, mirrored by
   other repositories, version-tracked,vocabulary-controlled, and citable.
   ICARUS hosts both legacy dataand new data in compliance with open access
   data mandates. Targeteddata discovery is available based on key
   experimental parameters,including organic reactants and mixtures that
   are managed using thePubChem chemical database, oxidant information,
   nitrogen oxide (NOx)content, alkylperoxy radical (RO2) fate, seed
   particleinformation, environmental conditions, and reaction categories.
   Adiscipline-specific repository such as ICARUS with high amounts
   ofmetadata works to support the evaluation and revision of
   atmosphericmodel mechanisms, intercomparison of data and models, and the
   developmentof new model frameworks that can have more predictive power
   in thecurrent and future atmosphere. The open accessibility and
   interactivenature of ICARUS data may also be useful for teaching, data
   mining,and training machine learning models.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Nguyen, TB (Corresponding Author), Univ Calif Davis, Dept Environm Toxicol, Davis, CA 95616 USA.
   Nguyen, Tran B.; Bates, Kelvin H., Univ Calif Davis, Dept Environm Toxicol, Davis, CA 95616 USA.
   Bates, Kelvin H., Harvard Univ, Ctr Environm, Cambridge, MA 02138 USA.
   Buenconsejo, Reina S.; Charan, Sophia M.; Kong, Weimeng; Seinfeld, John H., CALTECH, Div Chem \& Chem Engn, Pasadena, CA 91125 USA.
   Cavanna, Eric E.; Post, Jeroen J., Univ Calif Davis, Informat \& Educ Technol, Davis, CA 95616 USA.
   Cocker III, David R.; Le, Chen, Univ Calif Riverside, Dept Chem \& Environm Engn, Riverside, CA 92507 USA.
   Day, Douglas A.; DeVault, Marla P.; Finewax, Zachary; Handschy, Anne V.; Jimenez, Jose L.; Ziemann, Paul J., Univ Colorado Boulder, Cooperat Inst Res Environm Sci, Boulder, CO 80309 USA.
   DeVault, Marla P., Minnesota Dept Hlth, 625 Rober St N,POB 64975, St Paul, MN 55164 USA.
   Finewax, Zachary, NOAA, Chem Sci Lab, 325 Broadway R CSL, Boulder, CO 80305 USA.
   Day, Douglas A.; DeVault, Marla P.; Finewax, Zachary; Jimenez, Jose L.; Ziemann, Paul J., Univ Colorado Boulder, Dept Chem, Boulder, CO 80309 USA.
   Donahue, Neil M., Carnegie Mellon Univ, Dept Chem, Pittsburgh, PA 15213 USA.
   Donahue, Neil M.; Habib, Luke F., Carnegie Mellon Univ, Dept Chem Engn, Pittsburgh, PA 15213 USA.
   Donahue, Neil M., Carnegie Mellon Univ, Dept Engn \& Publ Policy, Pittsburgh, PA 15213 USA.
   Univ Texas Austin, McKetta Dept Chem Engn, Austin, TX 78712 USA.
   Natl Ctr Atmospher Res, Data Stewardship Engn Team, Boulder, CO 80307 USA.
   Hou, Chung-Yi S., Ronin Inst, 127 Haddon Pl, Montclair, NJ 07043 USA.
   Georgia Inst Technol, Sch Earth \& Atmospher Sci, Atlanta, GA 30332 USA.
   Joo, Taekyu, Yale Univ, POB 208236, New Haven, CT 06520 USA.
   Univ Calif Irvine, Dept Chem, Irvine, CA 92697 USA.
   Kong, Weimeng, Calif Air Resources Board, 1001 I St, Sacramento, CA 95814 USA.
   Georgia Inst Technol, Sch Chem \& Biomol Engn, Atlanta, GA 30332 USA.
   Georgia Inst Technol, Sch Civil \& Environm Engn, Atlanta, GA 30332 USA.
   Natl Ctr Atmospher Res, Atmospher Chem Observat \& Modeling, Boulder, CO 80305 USA.
   Univ Calif Davis, Air Qual Res Ctr, Davis, CA 95616 USA.
   Sturm, Patrick O., Univ Southern Calif, 3470 Trousdale Pkwy, Los Angeles, CA 90089 USA.
   CALTECH, Div Engn \& Appl Sci, Pasadena, CA 91125 USA.
   Zhang, Xuan, UC Merced, 5200 Lake Rd, Merced, CA 95343 USA.},
DOI = {10.1021/acsearthspacechem.3c00043},
EarlyAccessDate = {MAY 2023},
ISSN = {2472-3452},
Keywords = {atmospheric chamber; database; datarepository; data science; atmospheric
   chemistryand physics},
Keywords-Plus = {SECONDARY ORGANIC AEROSOL; MASTER CHEMICAL MECHANISM; OXIDATION FLOW
   REACTORS; GAS-PHASE REACTIONS; MCM V3 PART; TROPOSPHERIC DEGRADATION;
   PHOTOCHEMICAL DATA; RADICAL CHEMISTRY; PHOTOOXIDATION; PROTOCOL},
Research-Areas = {Chemistry; Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary; Geochemistry \& Geophysics},
Author-Email = {tbn@ucdavis.edu},
Affiliations = {University of California System; University of California Davis; Harvard
   University; California Institute of Technology; University of California
   System; University of California Davis; University of California System;
   University of California Riverside; University of Colorado System;
   University of Colorado Boulder; Minnesota Department of Health (MHD);
   National Oceanic Atmospheric Admin (NOAA) - USA; University of Colorado
   System; University of Colorado Boulder; Carnegie Mellon University;
   Carnegie Mellon University; Carnegie Mellon University; University of
   Texas System; University of Texas Austin; National Center Atmospheric
   Research (NCAR) - USA; University System of Georgia; Georgia Institute
   of Technology; Yale University; University of California System;
   University of California Irvine; University System of Georgia; Georgia
   Institute of Technology; University System of Georgia; Georgia Institute
   of Technology; National Center Atmospheric Research (NCAR) - USA;
   University of California System; University of California Davis;
   University of Southern California; California Institute of Technology;
   University of California System; University of California Merced},
ResearcherID-Numbers = {Jimenez, Jose L/A-5294-2008
   Atmospheric Particle Studies, Center for/AAR-6731-2020
   Nizkorodov, Sergey/I-4120-2014
   Nguyen, Tran B/E-9849-2012
   Nguyen, Tran/P-4902-2018
   Sturm, Patrick Obin/HKE-3951-2023},
ORCID-Numbers = {Jimenez, Jose L/0000-0001-6203-1847
   Nizkorodov, Sergey/0000-0003-0891-0052
   Nguyen, Tran/0000-0001-9206-4359
   Sturm, Patrick Obin/0000-0001-7361-9590},
Funding-Acknowledgement = {National Science Foundation, Directorate for Geosciences, Division of
   Atmospheric and Geospace Sciences, Atmospheric Chemistry Program
   {[}1740571, 1740552, 1740610, 1740640, 1740665, 1740587, 1740625,
   1740568]; California Agricultural Experiment Station through the USDA
   National Institute of Food and Agriculture {[}CAD-ETX-2699-H]; National
   Science Foundation},
Funding-Text = {We acknowledge funding from the National Science Foundation, Directorate
   for Geosciences, Division of Atmospheric and Geospace Sciences,
   Atmospheric Chemistry Program under the following grants: 1740571
   (Nguyen); 1740552 (Seinfeld); 1740610 (Jimenez, Ziemann); 1740640
   (Nizkorodov); 1740665 (Donahue, Robinson, Pandis); 1740587 (Hildebrandt
   Ruiz); 1740625 (Cocker); 1740568 (Ng). T.B.N. is also supported by the
   California Agricultural Experiment Station (grant no. CAD-ETX-2699-H)
   through the USDA National Institute of Food and Agriculture. The
   National Center for Atmospheric Research is operated by the University
   Corporation for Atmospheric Research, under the sponsorship of the
   National Science Foundation. We are grateful for the helpful feedback
   from our Data User test cohort: Prof. Alex Archibald at the University
   of Cambridge, and 12 other anonymous reviewers.},
Number-of-Cited-References = {66},
Times-Cited = {0},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {6},
Journal-ISO = {ACS Earth Space Chem.},
Doc-Delivery-Number = {J6XV4},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001015209000001},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000302750000002,
Author = {Kyzar, Evan and Zapolsky, Ivan and Green, Jeremy and Gaikwad, Siddharth
   and Pham, Mimi and Collins, Christopher and Roth, Andrew and Stewart,
   Adam Michael and St-Pierre, Paul and Hirons, Budd and Kalueff, Allan V.},
Title = {The Zebrafish Neurophenome Database (ZND): A Dynamic Open-Access
   Resource for Zebrafish Neurophenotypic Data},
Journal = {ZEBRAFISH},
Year = {2012},
Volume = {9},
Number = {1},
Pages = {8-14},
Month = {MAR},
Abstract = {Zebrafish (Danio rerio) are widely used in neuroscience research, where
   their utility as a model organism is rapidly expanding. Low cost, ease
   of experimental manipulations, and sufficient behavioral complexity make
   zebrafish a valuable tool for high-throughput studies in biomedicine. To
   complement the available repositories for zebrafish genetic information,
   there is a growing need for the collection of zebrafish neurobehavioral
   and neurological phenotypes. For this, we are establishing the Zebrafish
   Neurophenome Database (ZND; www.tulane.edu/similar to znpindex/similar
   to search) as a new dynamic online open-access data repository for
   behavioral and related physiological data. ZND, currently focusing on
   adult zebrafish, combines zebrafish neurophenotypic data with a simple,
   easily searchable user interface, which allow scientists to view and
   compare results obtained by other laboratories using various treatments
   in different testing paradigms. As a developing community effort, ZND is
   expected to foster innovative research using zebrafish by federating the
   growing body of zebrafish neurophenotypic data.},
Publisher = {MARY ANN LIEBERT, INC},
Address = {140 HUGUENOT STREET, 3RD FL, NEW ROCHELLE, NY 10801 USA},
Type = {Article},
Language = {English},
Affiliation = {Kalueff, AV (Corresponding Author), Tulane Univ, Sch Med, Dept Pharmacol, ZNRC, Room SL-83,1430 Tulane Ave, New Orleans, LA 70112 USA.
   Kyzar, Evan; Zapolsky, Ivan; Green, Jeremy; Gaikwad, Siddharth; Pham, Mimi; Collins, Christopher; Roth, Andrew; Stewart, Adam Michael; Kalueff, Allan V., Tulane Univ, Sch Med, Dept Pharmacol, ZNRC, New Orleans, LA 70112 USA.
   Kyzar, Evan; Zapolsky, Ivan; Green, Jeremy; Gaikwad, Siddharth; Pham, Mimi; Collins, Christopher; Roth, Andrew; Stewart, Adam Michael; Kalueff, Allan V., Tulane Univ, Sch Med, Neurosci Program, ZNRC, New Orleans, LA 70112 USA.
   St-Pierre, Paul; Hirons, Budd, Tulane Innovat Learning Ctr, New Orleans, LA USA.
   St-Pierre, Paul; Hirons, Budd, Howard Tilton Mem Lib, New Orleans, LA USA.},
DOI = {10.1089/zeb.2011.0725},
ISSN = {1545-8547},
EISSN = {1557-8542},
Keywords-Plus = {ONLINE MENDELIAN INHERITANCE; INFORMATION NETWORK ZFIN; ANXIETY-LIKE
   BEHAVIOR; MODEL ORGANISM; ADULT ZEBRAFISH; DRUG DISCOVERY; GENOME
   PROJECT; HUMAN-DISEASE; OMICS DATA; KNOWLEDGEBASE},
Research-Areas = {Developmental Biology; Zoology},
Web-of-Science-Categories  = {Developmental Biology; Zoology},
Author-Email = {avkalueff@gmail.com},
Affiliations = {Tulane University; Tulane University; Tulane University},
ResearcherID-Numbers = {Kalueff, Allan/AAB-8620-2022
   Kalueff, Allan V/B-3647-2010
   Gaikwad, Siddharth/HSF-9132-2023
   },
ORCID-Numbers = {Kalueff, Allan/0000-0002-7525-1950
   Kalueff, Allan V/0000-0002-7525-1950
   Gaikwad, Siddharth/0000-0001-6437-7016
   St-Pierre, Paul/0000-0001-6339-0964
   Zapolsky, Ivan/0000-0003-0174-6544
   Kyzar, Evan/0000-0002-7688-0281},
Funding-Acknowledgement = {Tulane University; Tulane Medical School Intramural and Pilot funds; LA
   Board of Regents P-Fund; NIDA R03 SOAR {[}DA030900-02]; Tulane
   University Innovative Learning Center; Tulane Neurophenotyping Platform;
   International Zebrafish Neuroscience Research Consortium},
Funding-Text = {This project is supported by Tulane University, Tulane Medical School
   Intramural and Pilot funds, LA Board of Regents P-Fund, and NIDA R03
   SOAR (DA030900-02) grants. Organizational and methodological support is
   provided by the Tulane University Innovative Learning Center, Tulane
   Neurophenotyping Platform, and the International Zebrafish Neuroscience
   Research Consortium. The authors thank R. Riehl, R. Razavi, A. Main, L.
   Monnig, K. Rhymes, M. Hook, I.. Bruce, C. Fryar, J. Hester, J. Raymond,
   S. Bagawandoss, and J. Enriquez (Tulane University) for their help with
   the initial phase of the ZND project. Help of Xiang Chen and colleagues
   from Tulane University's Innovative Learning Center is also greatly
   appreciated.},
Number-of-Cited-References = {101},
Times-Cited = {12},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Zebrafish},
Doc-Delivery-Number = {925GV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000302750000002},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000269652500465,
Author = {Venkatesan, A. and Goins, J. and Frohman, E. and Remington, G. and
   Sadiq, S. and Puccio, L. and Thrower, B. and Iski, E. and Riskind, P.
   and Weaver, J. and Campagnolo, D. and Bullock, B. and Kinkel, R. P. and
   Konkel, S. and Racke, M. and Hafer, L. and Vollmer, T. and Edwards, S.
   and Loud, S. and Mellor, A. and Schmidt, H.},
Title = {Growth and utilisation of an open-access, multidisciplinary,
   longitudinal sample and data repository for investigating multiple
   sclerosis and other demyelinating diseases},
Journal = {MULTIPLE SCLEROSIS},
Year = {2009},
Volume = {15},
Number = {9},
Pages = {S156},
Month = {SEP},
Note = {25th Congress of the
   European-Committee-for-Treatment-and-Research-in-Multiple-Sclerosis,
   Dusseldorf, GERMANY, SEP 09-12, 2009},
Organization = {European Comm Treatment \& Res Multiple Sclerosis},
Publisher = {SAGE PUBLICATIONS LTD},
Address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND},
Type = {Meeting Abstract},
Language = {English},
Affiliation = {Johns Hopkins Sch Med, Baltimore, MD USA.
   Univ Texas SW Med Ctr Dallas, Dallas, TX 75390 USA.
   Multiple Sclerosis Res Ctr, New York, NY USA.
   Shepherd Ctr, Atlanta, GA USA.
   Univ Massachusetts, Sch Med, Worcester, MA USA.
   Barrow Neurol Inst, Phoenix, AZ 85013 USA.
   Beth Israel Deaconess Med Ctr, Boston, MA 02215 USA.
   Ohio State Univ, Med Ctr, Columbus, OH 43210 USA.
   Accelerated Cure Project MS, Waltham, MA USA.},
ISSN = {1352-4585},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Clinical Neurology; Neurosciences},
Affiliations = {Johns Hopkins University; Johns Hopkins Medicine; University of Texas
   System; University of Texas Southwestern Medical Center Dallas;
   University of Massachusetts System; University of Massachusetts
   Worcester; Barrow Neurological Institute; Harvard University; Beth
   Israel Deaconess Medical Center; University System of Ohio; Ohio State
   University},
ResearcherID-Numbers = {Sadiq, Saud/AAA-9871-2020},
Number-of-Cited-References = {0},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Mult. Scler.},
Doc-Delivery-Number = {492JW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000269652500465},
DA = {2024-01-15},
}

@article{ WOS:000466818600051,
Author = {Diblen, Faruk and Attema, Jisk and Bakhshi, Rena and Caron, Sascha and
   Hendriks, Luc and Stienen, Bob},
Title = {SPOT: Open Source framework for scientific data repository and
   interactive visualization},
Journal = {SOFTWAREX},
Year = {2019},
Volume = {9},
Pages = {328-331},
Month = {JAN-JUN},
Abstract = {SPOT is an open source and free visual data analytics tool for
   multi-dimensional data-sets. Its web-based interface enables user to do
   a quick and interactive analysis of complex data. Various operations on
   data are implemented such as aggregation and filtering. The interface
   supports OpenGL acceleration, which makes the generated charts very
   responsive. In order to have scalability, the software also supports
   PostgreSQL as its database. It follows FAIR principles to allow reuse
   and comparison of the published data-sets. (C) 2019 The Authors.
   Published by Elsevier B.V.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Diblen, F; Attema, J (Corresponding Author), Netherlands eSci Ctr, Sci Pk 140, NL-1098 XG Amsterdam, Netherlands.
   Diblen, Faruk; Attema, Jisk; Bakhshi, Rena, Netherlands eSci Ctr, Sci Pk 140, NL-1098 XG Amsterdam, Netherlands.
   Caron, Sascha; Hendriks, Luc; Stienen, Bob, Radboud Univ Nijmegen, IMAPP, Nijmegen, Netherlands.},
DOI = {10.1016/j.softx.2019.04.006},
ISSN = {2352-7110},
Keywords = {Visualization; High-dimensional data; Theoretical models; Open data;
   FAIR; Particle physics},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Software Engineering},
Author-Email = {f.diblen@esciencecenter.nl
   j.attema@esciencecenter.nl
   r.bakhshi@esciencecenter.nl
   scaron@nikhef.nl
   luchendriks@gmail.com
   B.Stienen@science.ru.nl},
Affiliations = {Radboud University Nijmegen},
ORCID-Numbers = {Bakhshi, Rena/0000-0002-2932-3028
   Attema, Jisk/0000-0002-0948-1176},
Funding-Acknowledgement = {Netherlands eScience Center under the project iDark: The intelligent
   Dark Matter Survey},
Funding-Text = {This work is supported by the Netherlands eScience Center under the
   project iDark: The intelligent Dark Matter Survey.},
Number-of-Cited-References = {11},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {SoftwareX},
Doc-Delivery-Number = {HW6RS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000466818600051},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000331139800140,
Author = {Stachelscheid, Harald and Seltmann, Stefanie and Lekschas, Fritz and
   Fontaine, Jean-Fred and Mah, Nancy and Neves, Mariana and
   Andrade-Navarro, Miguel A. and Leser, Ulf and Kurtz, Andreas},
Title = {CellFinder: a cell data repository},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2014},
Volume = {42},
Number = {D1},
Pages = {D950-D958},
Month = {JAN},
Abstract = {CellFinder (http://www.cellfinder.org) is a comprehensive one-stop
   resource for molecular data characterizing mammalian cells in different
   tissues and in different development stages. It is built from carefully
   selected data sets stemming from other curated databases and the
   biomedical literature. To date, CellFinder describes 3394 cell types and
   50 951 cell lines. The database currently contains 3055 microscopic and
   anatomical images, 205 whole-genome expression profiles of 194
   cell/tissue types from RNA-seq and microarrays and 553 905 protein
   expressions for 535 cells/tissues. Text mining of a corpus of >2000
   publications followed by manual curation confirmed expression
   information on similar to 900 proteins and genes. CellFinder's data
   model is capable to seamlessly represent entities from single cells to
   the organ level, to incorporate mappings between homologous entities in
   different species and to describe processes of cell development and
   differentiation. Its ontological backbone currently consists of 204 741
   ontology terms incorporated from 10 different ontologies unified under
   the novel CELDA ontology. CellFinder's web portal allows searching,
   browsing and comparing the stored data, interactive construction of
   developmental trees and navigating the partonomic hierarchy of cells and
   tissues through a unique body browser designed for life scientists and
   clinicians.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Kurtz, A (Corresponding Author), Charite, Berlin Brandenburg Ctr Regenerat Med, D-13353 Berlin, Germany.
   Stachelscheid, Harald; Seltmann, Stefanie; Lekschas, Fritz; Kurtz, Andreas, Charite, Berlin Brandenburg Ctr Regenerat Med, D-13353 Berlin, Germany.
   Fontaine, Jean-Fred; Mah, Nancy; Andrade-Navarro, Miguel A., Max Delbruck Ctr Mol Med, D-13125 Berlin, Germany.
   Neves, Mariana; Leser, Ulf, Humboldt Univ, Inst Comp Sci, D-10099 Berlin, Germany.
   Kurtz, Andreas, Seoul Natl Univ, Coll Vet Med, Seoul 151742, South Korea.
   Kurtz, Andreas, Seoul Natl Univ, Res Inst Vet Sci, Seoul 151742, South Korea.},
DOI = {10.1093/nar/gkt1264},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENE-EXPRESSION; ONTOLOGY; TOOL; MICROARRAY; EVOLUTION; RESOURCE; MODEL},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {andreas.kurtz@charite.de},
Affiliations = {Free University of Berlin; Humboldt University of Berlin; Charite
   Universitatsmedizin Berlin; Helmholtz Association; Max Delbruck Center
   for Molecular Medicine; Humboldt University of Berlin; Seoul National
   University (SNU); Seoul National University (SNU)},
ResearcherID-Numbers = {Andrade, Miguel A/B-6565-2008
   Fontaine, Jean-Fred/GNP-2904-2022
   },
ORCID-Numbers = {Andrade, Miguel A/0000-0001-6650-1711
   Fontaine, Jean-Fred/0000-0002-1101-4091
   Mah, Nancy/0000-0002-1240-8076
   Neves, Mariana/0000-0002-6488-2394
   Stachelscheid, Harald/0000-0002-9283-4605
   Lekschas, Fritz/0000-0001-8432-4835
   Kurtz, Andreas/0000-0003-3301-6546
   Seltmann, Stefanie/0000-0002-8411-3226},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft {[}KU 851/3-1, LE 1428/3-1]; European
   Commission {[}334502]; Public Funds (Seoul National University)},
Funding-Text = {Deutsche Forschungsgemeinschaft {[}KU 851/3-1, LE 1428/3-1 to A. K. and
   U. L.] and the European Commission {[}334502 to A. K.]. Funding for open
   access charge: Public Funds (Seoul National University).},
Number-of-Cited-References = {49},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {AA5LF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000331139800140},
OA = {Green Published, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000562942600006,
Author = {Garcia, E. and Verdasco, J. E. and Lagana, A.},
Title = {Collisional O<sub>2</sub> + N<sub>2</sub> State-Selected Cross Sections
   for Open Science Cloud Reuse},
Journal = {JOURNAL OF PHYSICAL CHEMISTRY A},
Year = {2020},
Volume = {124},
Number = {32},
Pages = {6445-6457},
Month = {AUG 13},
Abstract = {In this paper, we report a quasi-classical trajectory study of the
   internal energy state specificity of dissociative O-2 + N-2 collision
   rates computed at high temperatures on an accurate potential energy
   surface (PES). This paper analyzes the outcomes of the trajectory
   calculations performed by explicitly considering the rotational state of
   the reactants and compares them with those of a previous study carried
   out by assuming a thermal rotational distribution. In particular, in
   order to quantify the deviation of the rotationally thermalized rates
   from the rotationally state-selected ones, we discuss here the
   properties of the corresponding state-specific and state-to-state cross
   sections with the support of both internuclear distance and bond-order
   reduced dimensionality representations of the isoenergetic contours of
   the PES. This allows us to single out a suitable bond-order-like process
   coordinate useful for modeling detailed dissociation cross sections and
   rate coefficients and relating them, as well, to some specific features
   of the PES. Furthermore, this is also shown to be useful for structuring
   data repositories of the molecular section of the European Open Science
   Cloud Project so as to obtain collaborative production, validation,
   reuse, and dissemination of chemical processes' knowledge and efficiency
   parameters.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Garcia, E (Corresponding Author), Univ Basque Country, Dept Quim Fis, UPV EHU, Vitoria 01006, Spain.
   Verdasco, J. E., Univ Complutense Madrid, Fac Quim, Dept Quim Fis, Madrid 28040, Spain.
   Lagana, A., Master UP Srl, I-06131 Perugia, Italy.
   Lagana, A., CNR SCITEC UOS Perugia, I-06123 Perugia, Italy.
   Garcia, E., Univ Basque Country, Dept Quim Fis, UPV EHU, Vitoria 01006, Spain.},
DOI = {10.1021/acs.jpca.0c04937},
ISSN = {1089-5639},
EISSN = {1520-5215},
Keywords-Plus = {POTENTIAL-ENERGY SURFACES; STATE VIBRATIONAL-RELAXATION; LONG-RANGE
   INTERACTION; GLOBAL FIT; FUNCTIONAL FORM; CROSS-SECTIONS; DISSOCIATION;
   N-2-N-2; O-2-O-2; OXYGEN},
Research-Areas = {Chemistry; Physics},
Web-of-Science-Categories  = {Chemistry, Physical; Physics, Atomic, Molecular \& Chemical},
Author-Email = {e.garcia@ehu.es},
Affiliations = {Complutense University of Madrid; Consiglio Nazionale delle Ricerche
   (CNR); Istituto di Scienze Tecnologie Chimiche ``Giulio Natta{''}
   (SCITEC-CNR); University of Basque Country},
ResearcherID-Numbers = {Garcia, Ernesto/A-2635-2015
   Verdasco, Juan E./AAS-9174-2021
   Lagana, Antonio/E-8215-2014},
ORCID-Numbers = {Garcia, Ernesto/0000-0001-8778-8141
   Verdasco, Juan E./0000-0003-2585-1699
   Lagana, Antonio/0000-0002-3886-7342},
Funding-Acknowledgement = {MINECO/FEDER of Spain {[}PGC2018-096444-BI00]},
Funding-Text = {E.G. and J.E.V. acknowldedge the financial support from the MINECO/FEDER
   of Spain under grant PGC2018-096444-BI00. The authors also thank the
   Oklahoma University Supercomputing Center for Education \& Research
   (OSCER) and the European Grid Infrastructure (EGI) through COMPCHEM
   Virtual Organization for providing computing resources and services.},
Number-of-Cited-References = {71},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {13},
Journal-ISO = {J. Phys. Chem. A},
Doc-Delivery-Number = {NE9RW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000562942600006},
DA = {2024-01-15},
}

@article{ WOS:000336502400035,
Author = {Fouke, Sarah Jost and Benzinger, Tammie L. and Milchenko, Mikhail and
   LaMontagne, Pamela and Shimony, Joshua S. and Chicoine, Michael R. and
   Rich, Keith M. and Kim, Albert H. and Leuthardt, Eric C. and Keogh, Bart
   and Marcus, Daniel S.},
Title = {The Comprehensive Neuro-Oncology Data Repository (CONDR): A Research
   Infrastructure to Develop and Validate Imaging Biomarkers},
Journal = {NEUROSURGERY},
Year = {2014},
Volume = {74},
Number = {1},
Pages = {88-98},
Month = {JAN},
Abstract = {BACKGROUND: Advanced imaging methods have the potential to serve as
   quantitative biomarkers in neuro-oncology research. However, a lack of
   standardization of image acquisition, processing, and analysis limits
   their application in clinical research. Standardization of these methods
   and an organized archival platform are required to better validate and
   apply these markers in research settings and, ultimately, in clinical
   practice.
   OBJECTIVE: The primary objective of the Comprehensive Neuro-oncology
   Data Repository (CONDR) is to develop a data set for assessing and
   validating advanced imaging methods in patients diagnosed with brain
   tumors. As a secondary objective, informatics resources will be
   developed to facilitate the integrated collection, processing, and
   analysis of imaging, tissue, and clinical data in multicenter clinical
   trials. Finally, CONDR data and informatics resources will be shared
   with the research community for further analysis.
   METHODS: CONDR will enroll 200 patients diagnosed with primary brain
   tumors. Clinical, imaging, and tissue-based data are obtained from
   patients serially, beginning with diagnosis and continuing over the
   course of their treatment. The CONDR imaging protocol includes
   structural and functional sequences, including diffusion-and
   perfusion-weighted imaging. All data are managed within an XNAT-based
   informatics platform. Imaging markers are assessed by correlating image
   and spatially aligned pathological markers and a variety of clinical
   markers.
   EXPECTED OUTCOMES: CONDR will generate data for developing and
   validating imaging markers of primary brain tumors, including
   multispectral and probabilistic maps.
   DISCUSSION: CONDR implements a novel, open-research model that will
   provide the research community with both open-access data and
   open-source informatics resources.},
Publisher = {OXFORD UNIV PRESS INC},
Address = {JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
Type = {Article},
Language = {English},
Affiliation = {Fouke, SJ (Corresponding Author), Swedish Med Ctr, Study PI, 550 17th Ave, Seattle, WA 98122 USA.
   Fouke, Sarah Jost, Swedish Med Ctr, Dept Neurol Surg, Seattle, WA 98122 USA.
   Benzinger, Tammie L.; Milchenko, Mikhail; LaMontagne, Pamela; Shimony, Joshua S.; Marcus, Daniel S., Washington Univ, Sch Med, Dept Radiol, St Louis, MO 63110 USA.
   Chicoine, Michael R.; Rich, Keith M.; Kim, Albert H.; Leuthardt, Eric C., Washington Univ, Sch Med, Dept Neurol Surg, St Louis, MO USA.
   Keogh, Bart, Swedish Neurosci Inst, Seattle, WA USA.
   Keogh, Bart, Radia PS, Everett, WA USA.},
DOI = {10.1227/NEU.0000000000000201},
ISSN = {0148-396X},
EISSN = {1524-4040},
Keywords = {Brain tumors; Database; Diffusion; Gliomas; Magnetic resonance imaging;
   Perfusion},
Keywords-Plus = {POSITRON-EMISSION-TOMOGRAPHY; GLIOMAS RESPONSE ASSESSMENT; FUNCTIONAL
   DIFFUSION MAPS; CEREBRAL BLOOD-VOLUME; BRAIN-TUMORS; PROGRESSION-FREE;
   GRADE GLIOMAS; MR PERFUSION; SURVIVAL; THERAPY},
Research-Areas = {Neurosciences \& Neurology; Surgery},
Web-of-Science-Categories  = {Clinical Neurology; Surgery},
Author-Email = {sarah.fouke@swedish.org},
Affiliations = {Swedish Medical Center; Washington University (WUSTL); Washington
   University (WUSTL); Swedish Medical Center},
ResearcherID-Numbers = {Benzinger, Tammie/L-6104-2013
   Kim, Albert H./HGF-0057-2022
   },
ORCID-Numbers = {Benzinger, Tammie/0000-0002-8114-0552
   LaMontagne, Pamela/0000-0002-6752-8518},
Funding-Acknowledgement = {NIH/National Institute of Neurological Disorders and Stroke
   {[}R01NS066905]},
Funding-Text = {This study was supported by the NIH/National Institute of Neurological
   Disorders and Stroke (R01NS066905). The authors have no personal,
   financial, or institutional interest in any of the drugs, materials, or
   devices described in this article.},
Number-of-Cited-References = {55},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Neurosurgery},
Doc-Delivery-Number = {AH9YQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000336502400035},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000686322300001,
Author = {Vazquez, Enrique and Gouraud, Henri and Naudet, Florian and Gross, Cary
   P. and Krumholz, Harlan M. and Ross, Joseph S. and Wallach, Joshua D.},
Title = {Characteristics of available studies and dissemination of research using
   major clinical data sharing platforms},
Journal = {CLINICAL TRIALS},
Year = {2021},
Volume = {18},
Number = {6},
Pages = {657-666},
Month = {DEC},
Abstract = {Background/Aims: Over the past decade, numerous data sharing platforms
   have been launched, providing access to de-identified individual
   patient-level data and supporting documentation. We evaluated the
   characteristics of prominent clinical data sharing platforms, including
   types of studies listed as available for request, data requests
   received, and rates of dissemination of research findings from data
   requests.
   Methods: We reviewed publicly available information listed on the
   websites of six prominent clinical data sharing platforms: Biological
   Specimen and Data Repository Information Coordinating Center,
   ClinicalStudyDataRequest.com, Project Data Sphere, Supporting Open
   Access to Researchers-Bristol Myers Squibb, Vivli, and the Yale Open
   Data Access Project. We recorded key platform characteristics, including
   listed studies and available supporting documentation, information on
   the number and status of data requests, and rates of dissemination of
   research findings from data requests (i.e. publications in a
   peer-reviewed journals, preprints, conference abstracts, or results
   reported on the platform's website).
   Results: The number of clinical studies listed as available for request
   varied among five data sharing platforms: Biological Specimen and Data
   Repository Information Coordinating Center (n = 219),
   ClinicalStudyDataRequest.com (n = 2,897), Project Data Sphere (n = 154),
   Vivli (n = 5426), and the Yale Open Data Access Project (n = 395);
   Supporting Open Access to Researchers did not provide a list of Bristol
   Myers Squibb studies available for request. Individual patient-level
   data were nearly always reported as being available for request, as
   opposed to only Clinical Study Reports (Biological Specimen and Data
   Repository Information Coordinating Center = 211/219 (96.3\%);
   ClinicalStudyDataRequest.com = 2884/2897 (99.6\%); Project Data Sphere =
   154/154 (100.0\%); and the Yale Open Data Access Project = 355/395
   (89.9\%)); Vivli did not provide downloadable study metadata. Of 1201
   data requests listed on ClinicalStudyData Request.com, Supporting Open
   Access to Researchers-Bristol Myers Squibb, Vivli, and the Yale Open
   Data Access Project platforms, 586 requests (48.8\%) were approved (i.e.
   data access granted). The majority were for secondary analyses and/or
   developing/validating methods (ClinicalStudyDataRequest.com = 262/313
   (83.7\%); Supporting Open Access to Researchers-Bristol Myers Squibb =
   22/30 (73.3\%); Vivli = 63/84 (75.0\%); the Yale Open Data Access
   Project = 111/159 (69.8\%)); four were for re-analyses or corroborations
   of previous research findings (ClinicalStudyDataRequest. corn = 3/313
   (1.0\%) and the Yale Open Data Access Project = 1/159 (0.6\%)).
   Ninety-five (16.1\%) approved data requests had results disseminated via
   peer-reviewed publications (ClinicalStudyDataRequest.com = 61/313
   (19.5\%); Supporting Open Access to Researchers-Bristol Myers Squibb =
   3/30 (10.0\%); Vivli = 4/84 (4.8\%); the Yale Open Data Access Project =
   27/159 (17.0\%)). Forty-two (6.8\%) additional requests reported results
   through preprints, conference abstracts, or on the platform's website
   (ClinicalStudyDataRequest.com = 12/ 313 (3.8\%); Supporting Open Access
   to Researchers-Bristol Myers Squibb = 3/30 (10.0\%); Vivli = 2/84
   (2.4\%); Yale Open Data Access Project = 25/159 (15.7\%)).
   Conclusion: Across six prominent clinical data sharing platforms,
   information on studies and request metrics varied in availability and
   format. Most data requests focused on secondary analyses and
   approximately one-quarter of all approved requests publicly disseminated
   their results. To further promote the use of shared clinical data,
   platforms should increase transparency, consistently clarify the
   availability of the listed studies and supporting documentation, and
   ensure that research findings from data requests are disseminated.},
Publisher = {SAGE PUBLICATIONS LTD},
Address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Wallach, JD (Corresponding Author), Yale Sch Publ Hlth, 60 Coll St,Floor 4,Room 411, New Haven, CT 06510 USA.
   Vazquez, Enrique, Yale Coll, New Haven, CT USA.
   Gouraud, Henri; Naudet, Florian, Univ Rennes, CHU Rennes, INSERM, Ctr Invest Clin Rennes, Rennes, France.
   Gross, Cary P.; Ross, Joseph S., Yale Sch Med, Sect Gen Internal Med, New Haven, CT USA.
   Gross, Cary P., Yale Univ, Canc Outcomes Publ Policy \& Effectiveness Res COP, New Haven, CT USA.
   Gross, Cary P., Yale Sch Publ Hlth, Dept Chron Dis Epidemiol, New Haven, CT USA.
   Krumholz, Harlan M., Yale Sch Med, Sect Cardiovasc Med, New Haven, CT USA.
   Krumholz, Harlan M.; Ross, Joseph S., Yale New Haven Med Ctr, Ctr Outcomes Res \& Evaluat, 20 York St, New Haven, CT 06504 USA.
   Krumholz, Harlan M.; Ross, Joseph S., Yale Sch Publ Hlth, Dept Hlth Policy \& Management, New Haven, CT USA.
   Wallach, Joshua D., Yale Sch Publ Hlth, Dept Environm Hlth Sci, New Haven, CT USA.},
DOI = {10.1177/17407745211038524},
EarlyAccessDate = {AUG 2021},
ISSN = {1740-7745},
EISSN = {1740-7753},
Keywords = {Clinical trials; transparency; data sharing},
Keywords-Plus = {OPEN ACCESS PLATFORMS; OPEN SCIENCE; TRIAL},
Research-Areas = {Research \& Experimental Medicine},
Web-of-Science-Categories  = {Medicine, Research \& Experimental},
Author-Email = {joshua.wallach@yale.edu},
Affiliations = {Yale University; Institut National de la Sante et de la Recherche
   Medicale (Inserm); Universite de Rennes; CHU Rennes; Yale University;
   Yale University; Yale University; Yale University; Yale University; Yale
   University},
ResearcherID-Numbers = {Naudet, Florian/H-5644-2019
   , Harlan/AAI-2875-2020
   },
ORCID-Numbers = {Naudet, Florian/0000-0003-3760-3801
   Ross, Joseph/0000-0002-9218-3320
   Wallach, Joshua/0000-0002-2816-6905},
Funding-Acknowledgement = {2020 Yale College Dean's Fellowship; 2020 Grace Hopper Richter
   Fellowship; National Institute on Alcohol Abuse and Alcoholism of the
   National Institutes of Health {[}K01AA028258]},
Funding-Text = {The author(s) disclosed receipt of the following financial support for
   the research, authorship, and/or publication of this article: Mr E.V.
   received financial support from the 2020 Yale College Dean's Fellowship
   and the 2020 Grace Hopper Richter Fellowship. Dr J.D.W. is supported by
   the National Institute on Alcohol Abuse and Alcoholism of the National
   Institutes of Health under award K01AA028258. The content is solely the
   responsibility of the authors and does not necessarily represent the
   official views of the National Institutes of Health.},
Number-of-Cited-References = {29},
Times-Cited = {13},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Clin. Trials},
Doc-Delivery-Number = {WW8BA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000686322300001},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000633030400010,
Author = {Loeffler, Felicitas and Wesp, Valentin and Koenig-Ries, Birgitta and
   Klan, Friederike},
Title = {Dataset search in biodiversity research: Do metadata in data
   repositories reflect scholarly information needs?},
Journal = {PLOS ONE},
Year = {2021},
Volume = {16},
Number = {3},
Month = {MAR 24},
Abstract = {The increasing amount of publicly available research data provides the
   opportunity to link and integrate data in order to create and prove
   novel hypotheses, to repeat experiments or to compare recent data to
   data collected at a different time or place. However, recent studies
   have shown that retrieving relevant data for data reuse is a
   time-consuming task in daily research practice. In this study, we
   explore what hampers dataset retrieval in biodiversity research, a field
   that produces a large amount of heterogeneous data. In particular, we
   focus on scholarly search interests and metadata, the primary source of
   data in a dataset retrieval system. We show that existing metadata
   currently poorly reflect information needs and therefore are the biggest
   obstacle in retrieving relevant data. Our findings indicate that for
   data seekers in the biodiversity domain environments, materials and
   chemicals, species, biological and chemical processes, locations, data
   parameters and data types are important information categories. These
   interests are well covered in metadata elements of domain-specific
   standards. However, instead of utilizing these standards, large data
   repositories tend to use metadata standards with domain-independent
   metadata fields that cover search interests only to some extent. A
   second problem are arbitrary keywords utilized in descriptive fields
   such as title, description or subject. Keywords support scholars in a
   full text search only if the provided terms syntactically match or their
   semantic relationship to terms used in a user query is known.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Löffler, F (Corresponding Author), Friedrich Schiller Univ Jena, Dept Math \& Comp Sci, Heinz Nixdorf Chair Distributed Informat Syst, Jena, Germany.
   Loeffler, Felicitas; Wesp, Valentin; Koenig-Ries, Birgitta, Friedrich Schiller Univ Jena, Dept Math \& Comp Sci, Heinz Nixdorf Chair Distributed Informat Syst, Jena, Germany.
   Koenig-Ries, Birgitta; Klan, Friederike, Michael Stifel Ctr Data Driven \& Simulat Sci, Jena, Germany.
   Koenig-Ries, Birgitta, German Ctr Integrat Biodivers Res iDiv, Halle, Germany.
   Klan, Friederike, German Aerosp Ctr, DLR Inst Data Sci, Citizen Sci Grp, Jena, Germany.},
DOI = {10.1371/journal.pone.0246099},
Article-Number = {e0246099},
ISSN = {1932-6203},
Keywords-Plus = {ANNOTATION; ECOLOGY},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {felicitas.loeffler@uni-jena.de},
Affiliations = {Friedrich Schiller University of Jena; Helmholtz Association; German
   Aerospace Centre (DLR)},
ORCID-Numbers = {Klan, Friederike/0000-0002-1856-7334
   Konig-Ries, Birgitta/0000-0002-2382-9722
   Wesp, Valentin/0000-0002-8601-6032
   Loffler, Felicitas/0000-0001-6423-7427},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft (DFG) {[}229241684, 218627073,
   433052568]},
Funding-Text = {We acknowledge the Collaborative Research Centre AquaDiva (CRC 1076
   AquaDiva, DFG Project Number: 218627073) of the Friedrich Schiller
   University Jena, the GFBio project (DFG Project Number: 229241684) and
   the Open Access Publication Fund of the Thueringer Universitaetsund
   Landesbibliothek Jena (DFG Project Number: 433052568), all funded by the
   Deutsche Forschungsgemeinschaft (DFG). The funder had no role in study
   design, data collection and analysis, decision to publish, or
   preparation of the manuscript.},
Number-of-Cited-References = {73},
Times-Cited = {10},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {15},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {RC8FS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000633030400010},
OA = {Green Published, gold, Green Submitted, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000908485500001,
Author = {Gries, Corinna and Hanson, Paul C. and O'Brien, Margaret and Servilla,
   Mark and Vanderbilt, Kristin and Waide, Robert},
Title = {The Environmental Data Initiative: Connecting the past to the future
   through data reuse},
Journal = {ECOLOGY AND EVOLUTION},
Year = {2023},
Volume = {13},
Number = {1},
Month = {JAN},
Abstract = {The Environmental Data Initiative (EDI) is a trustworthy, stable data
   repository, and data management support organization for the
   environmental scientist. In a bottom-up community process, EDI was built
   with the premise that freely and easily available data are necessary to
   advance the understanding of complex environmental processes and change,
   to improve transparency of research results, and to democratize
   ecological research. EDI provides tools and support that allow the
   environmental researcher to easily integrate data publishing into the
   research workflow. Almost ten years since going into production, we
   analyze metadata to provide a general description of EDI's collection of
   data and its data management philosophy and placement in the repository
   landscape. We discuss how comprehensive metadata and the repository
   infrastructure lead to highly findable, accessible, interoperable, and
   reusable (FAIR) data by evaluating compliance with specific community
   proposed FAIR criteria. Finally, we review measures and patterns of data
   (re)use, assuring that EDI is fulfilling its stated premise.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Gries, C (Corresponding Author), Univ Wisconsin, Ctr Limnol, Madison, WI 53706 USA.
   Gries, Corinna; Hanson, Paul C., Univ Wisconsin, Ctr Limnol, Madison, WI 53706 USA.
   O'Brien, Margaret, Univ Calif Santa Barbara, Marine Sci Inst, Santa Barbara, CA USA.
   Servilla, Mark; Vanderbilt, Kristin; Waide, Robert, Univ New Mexico, Dept Biol, Albuquerque, NM USA.},
DOI = {10.1002/ece3.9592},
Article-Number = {e9592},
ISSN = {2045-7758},
Keywords = {data reuse; environmental data repository; FAIR data; metadata; open
   science},
Keywords-Plus = {MANAGEMENT},
Research-Areas = {Environmental Sciences \& Ecology; Evolutionary Biology},
Web-of-Science-Categories  = {Ecology; Evolutionary Biology},
Author-Email = {cgries@wisc.edu},
Affiliations = {University of Wisconsin System; University of Wisconsin Madison;
   University of California System; University of California Santa Barbara;
   University of New Mexico},
ResearcherID-Numbers = {Hanson, Paul Ronald/HPH-6371-2023
   },
ORCID-Numbers = {Hanson, Paul/0000-0001-8533-6061
   Servilla, Mark/0000-0002-3192-7306
   Vanderbilt, Kristin/0000-0003-1439-2204
   Gries, Corinna/0000-0002-9091-6543
   O'Brien, Margaret/0000-0002-1693-8322},
Funding-Acknowledgement = {National Science Foundation;  {[}1931143];  {[}1931174]},
Funding-Text = {ACKNOWLEDGMENTS This work was supported by National Science Foundation
   awards \#1931143 and \#1931174.},
Number-of-Cited-References = {69},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Ecol. Evol.},
Doc-Delivery-Number = {7P1PK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000908485500001},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000328612800001,
Author = {Bujan, David and Martin, David and Torices, Ortzi and Lopez-de-Ipina,
   Diego and Lamsfus, Carlos and Abaitua, Joseba and Alzua-Sorzabal,
   Aurkene},
Title = {Context Management Platform for Tourism Applications},
Journal = {SENSORS},
Year = {2013},
Volume = {13},
Number = {7},
Pages = {8060-8078},
Month = {JUL},
Abstract = {The notion of context has been widely studied and there are several
   authors that have proposed different definitions of context. However,
   context has not been widely studied in the framework of human mobility
   and the notion of context has been imported directly from other
   computing fields without specifically addressing the tourism domain
   requirements. In order to store and manage context information a context
   data model and a context management platform are needed. Ontologies have
   been widely used in context modelling, but many of them are designed to
   be applied in general ubiquitous computing environments, do not contain
   specific concepts related to the tourism domain or some approaches do
   not contain enough concepts to represent context information related to
   the visitor on the move. That is why we propose a new approach to
   provide a better solution to model context data in tourism environments,
   adding more value to our solution reusing data about tourist resources
   from an Open Data repository and publishing it as Linked Data. We also
   propose the architecture for a context information management platform
   based on this context data model.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Buján, D (Corresponding Author), Univ Deusto, DeustoTech, Deusto Inst Technol, Avda Univ 24, Bilbao 48007, Spain.
   Bujan, David; Lopez-de-Ipina, Diego; Abaitua, Joseba, Univ Deusto, DeustoTech, Deusto Inst Technol, Bilbao 48007, Spain.
   Martin, David; Torices, Ortzi; Lamsfus, Carlos; Alzua-Sorzabal, Aurkene, CICtourGUNE, Cooperat Res Ctr Tourism, Donostia San Sebastian 20009, Spain.},
DOI = {10.3390/s130708060},
EISSN = {1424-8220},
Keywords = {context modelling; knowledge representation and management; ontologies;
   Open Data; Linked Data; tourism},
Research-Areas = {Chemistry; Engineering; Instruments \& Instrumentation},
Web-of-Science-Categories  = {Chemistry, Analytical; Engineering, Electrical \& Electronic;
   Instruments \& Instrumentation},
Author-Email = {david.bujan@deusto.es
   DavidMartin@tourgune.org
   OrtziTorices@tourgune.org
   dipina@deusto.es
   CarlosLamsfus@tourgune.org
   joseba.abaitua@deusto.es
   AurkeneAlzua@tourgune.org},
Affiliations = {University of Deusto},
ResearcherID-Numbers = {Buján-Carballal, David/L-2136-2014
   Abaitua, Joseba/R-5642-2019
   López-de-Ipiña, Diego/A-9651-2012
   Abaitua, Joseba/I-1554-2016
   Buján-Carballal, David/ABA-7964-2021
   Alzua-Sorzabal, Aurkene/K-7139-2017},
ORCID-Numbers = {Buján-Carballal, David/0000-0002-4300-4760
   Abaitua, Joseba/0000-0001-6957-8511
   López-de-Ipiña, Diego/0000-0001-8055-6823
   Abaitua, Joseba/0000-0001-6957-8511
   Buján-Carballal, David/0000-0002-4300-4760
   Alzua-Sorzabal, Aurkene/0000-0002-6058-9537},
Funding-Acknowledgement = {Etorgai research program from the Basque Government {[}ER-2010/00005]},
Funding-Text = {This paper is supported by Etorgai research program from the Basque
   Government, which provides funds to the TourExp project (ER-2010/00005).},
Number-of-Cited-References = {25},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Sensors},
Doc-Delivery-Number = {274NI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000328612800001},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000374650700002,
Author = {Kilic, Sefa and Sagitova, Dinara M. and Wolfish, Shoshannah and Bely,
   Benoit and Courtot, Melanie and Ciufo, Stacy and Tatusova, Tatiana and
   O'Donovan, Claire and Chibucos, Marcus C. and Martin, Maria J. and
   Erill, Ivan},
Title = {From data repositories to submission portals: rethinking the role of
   domain-specific databases in CollecTF},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2016},
Month = {APR 25},
Abstract = {Domain-specific databases are essential resources for the biomedical
   community, leveraging expert knowledge to curate published literature
   and provide access to referenced data and knowledge. The limited scope
   of these databases, however, poses important challenges on their
   infrastructure, visibility, funding and usefulness to the broader
   scientific community. CollecTF is a community-oriented database
   documenting experimentally validated transcription factor (TF)-binding
   sites in the Bacteria domain. In its quest to become a community
   resource for the annotation of transcriptional regulatory elements in
   bacterial genomes, CollecTF aims to move away from the conventional
   data-repository paradigm of domain-specific databases. Through the
   adoption of well-established ontologies, identifiers and collaborations,
   CollecTF has progressively become also a portal for the annotation and
   submission of information on transcriptional regulatory elements to
   major biological sequence resources (RefSeq, UniProtKB and the Gene
   Ontology Consortium). This fundamental change in database conception
   capitalizes on the domain-specific knowledge of contributing communities
   to provide high-quality annotations, while leveraging the availability
   of stable information hubs to promote long-term access and provide
   high-visibility to the data. As a submission portal, CollecTF generates
   TF-binding site information through direct annotation of RefSeq genome
   records, definition of TF-based regulatory networks in UniProtKB entries
   and submission of functional annotations to the Gene Ontology. As a
   database, CollecTF provides enhanced search and browsing, targeted data
   exports, binding motif analysis tools and integration with motif
   discovery and search platforms. This innovative approach will allow
   CollecTF to focus its limited resources on the generation of
   high-quality information and the provision of specialized access to the
   data.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Erill, I (Corresponding Author), Univ Maryland Baltimore Cty, Dept Biol Sci, 1000 Hilltop Circle, Baltimore, MD 21250 USA.
   Kilic, Sefa; Sagitova, Dinara M.; Erill, Ivan, Univ Maryland Baltimore Cty, Dept Biol Sci, 1000 Hilltop Circle, Baltimore, MD 21250 USA.
   Wolfish, Shoshannah; Chibucos, Marcus C., Univ Maryland, Sch Med, Inst Genome Sci, Baltimore, MD 21201 USA.
   Bely, Benoit; Courtot, Melanie; O'Donovan, Claire; Martin, Maria J., European Bioinformat Inst, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Ciufo, Stacy; Tatusova, Tatiana, NIH, Natl Ctr Biotechnol Informat, Natl Lib Med, Bldg 38A, Bethesda, MD 20894 USA.
   Chibucos, Marcus C., Univ Maryland, Sch Med, Dept Microbiol \& Immunol, Baltimore, MD 21201 USA.},
DOI = {10.1093/database/baw055},
Article-Number = {baw055},
ISSN = {1758-0463},
Keywords-Plus = {SEQUENCES; ONTOLOGY; TOOL; DNA},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {erill@umbc.edu},
Affiliations = {University System of Maryland; University of Maryland Baltimore County;
   University System of Maryland; University of Maryland Baltimore;
   Wellcome Trust Sanger Institute; European Molecular Biology Laboratory
   (EMBL); National Institutes of Health (NIH) - USA; NIH National Library
   of Medicine (NLM); University System of Maryland; University of Maryland
   Baltimore},
ResearcherID-Numbers = {Chibucos, Marcus/B-1506-2015
   Erill, Ivan/H-9405-2015
   Martín, María/HDL-9512-2022
   },
ORCID-Numbers = {Chibucos, Marcus/0000-0001-9586-0780
   Erill, Ivan/0000-0002-7280-7191
   Courtot, Melanie/0000-0002-9551-6370
   Bely, Benoit/0000-0002-0029-9693
   O'Donovan, Claire/0000-0001-8051-7429
   Martin, Maria-Jesus/0000-0001-5454-2815},
Funding-Acknowledgement = {US National Science Foundation Division of Molecular and Cellular
   Biosciences {[}MCB-1158056]; US National Institutes of Health/National
   Human Genome Research Institute {[}U41HG007822, U41HG002273]; US
   National Science Foundation Division of Biological Infrastructure Award
   {[}DBI-1458400]; European Molecular Biology Laboratory core funds.
   Funding for open access charge: US National Sciences Foundation
   {[}MCB-1158056]; Direct For Biological Sciences; Div Of Biological
   Infrastructure {[}1458400] Funding Source: National Science Foundation;
   Direct For Biological Sciences; Div Of Molecular and Cellular Bioscience
   {[}1158056] Funding Source: National Science Foundation},
Funding-Text = {This work was funded by the US National Science Foundation Division of
   Molecular and Cellular Biosciences award MCB-1158056 (University of
   Maryland Baltimore County), the US National Institutes of
   Health/National Human Genome Research Institute grants U41HG007822 and
   U41HG002273 (European Bioinformatics Institute - European Molecular
   Biology Laboratory), the US National Science Foundation Division of
   Biological Infrastructure Award DBI-1458400 (University of Maryland at
   Baltimore) and by the European Molecular Biology Laboratory core funds.
   Funding for open access charge: US National Sciences Foundation
   {[}MCB-1158056].},
Number-of-Cited-References = {30},
Times-Cited = {13},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Database},
Doc-Delivery-Number = {DK1CS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000374650700002},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000832988800005,
Author = {Elger, Kirsten and ter Maat, Geertje and Caldeira, Rita and Cimarelli,
   Corrado and Corbi, Fabio and Dominguez, Stephane and Drury, Martyn and
   Funiciello, Francesca and Lange, Otto and Ougier-Simonin, Audrey and
   Rosenau, Matthias and Wessels, Richard and Willingshofer, Ernst and
   Winkler, Aldo},
Title = {The EPOS Multi-Scale Laboratories: A FAIR Framework for Stimulating Open
   Science Practice across European Earth Sciences Laboratories},
Journal = {ANNALS OF GEOPHYSICS},
Year = {2022},
Volume = {65},
Number = {3, SI},
Abstract = {The Multi-scale Laboratories (MSL) are a network of European
   laboratories bringing together the scientific fields of analogue
   modeling, paleomagnetism, experimental rock and melt physics,
   geochemistry and microscopy. MSL is one of nine (see below) Thematic
   Core Services (TCS) of the European Plate Observing System (EPOS). The
   overarching goal of EPOS is to establish a comprehensive
   multidisciplinary research platform for the Earth sciences in Europe. It
   aims at facilitating the integrated use of data, models, and facilities,
   from both existing and new distributed pan European Research
   Infrastructures, allowing open access and transparent use of data.
   The TCS MSL network allows researchers to collaborate with other labs
   and scientists. By becoming part of the rapidly growing TCS MSL network,
   new laboratories are offered a platform to showcase their research data
   output, laboratory equipment and information, and the opportunity to
   open laboratories to guest researchers through the Transnational Access
   (TNA) program.
   The EPOS Multi-scale laboratories offer researchers a fully operational
   data publication chain tailored to the specific needs of laboratory
   research, from a bespoke metadata editor, through dedicated,
   (domain-specific) data repositories, to the MSL Portal showcasing these
   citable data publications. During this process the data publications are
   assigned with digital object identidiers (DOI), published with open
   licenses (e.g. CC BY 4.0) and described with standardized and
   machine-readable rich metadata (following the FAIR Principles to make
   research data Findable, Accessible, Interoperable and Reusable. The TCS
   MSL is currently working on linking these data publications to the EPOS
   Central Portal1, the main discovery and access point for European
   multi-disciplinary data, and on increasing the number of connected data
   repositories.},
Publisher = {IST NAZIONALE DI GEOFISICA E VULCANOLOGIA},
Address = {VIA VIGNA MURATA 605, ROME, 00143, ITALY},
Type = {Article},
Language = {English},
Affiliation = {Elger, K (Corresponding Author), GFZ German Res Ctr Geosci, D-14473 Potsdam, Germany.
   Elger, Kirsten; Rosenau, Matthias, GFZ German Res Ctr Geosci, D-14473 Potsdam, Germany.
   ter Maat, Geertje; Drury, Martyn; Wessels, Richard; Willingshofer, Ernst, Univ Utrecht, Princetonlaan 8a, NL-3584 CB Utrecht, Netherlands.
   Caldeira, Rita, Lab Nacl Energia \& Geol, Estr Portela Bairro Zambujal Apartado 7586, P-2610999 Alfragide, Amadora, Portugal.
   Cimarelli, Corrado, Ludwig Maximilians Univ Munchen, Theresienstr 41, D-80333 Munich, Germany.
   Corbi, Fabio, Sapienza Univ Roma, CNR, Ist Geol Ambientale \& Geoingn, Dipartimento Sci Terra, Rome, Italy.
   Dominguez, Stephane, Univ Montpellier, Geosci Montpellier, Pl Eugene Bataillon, F-34095 Montpellier 05, France.
   Funiciello, Francesca, Univ Roma TRE, Dipartimento Sci, Largo San Leonardo Murialdo 1, I-00146 Rome, Italy.
   Lange, Otto, Utrecht Univ Lib, Heidelberglaan 3, NL-3584 CS Utrecht, Netherlands.
   Ougier-Simonin, Audrey, British Geol Survey, Nicker Hill, Keyworth, Notts, England.
   Winkler, Aldo, Ist Nazl Geofis \& Vulcanol, Rome, Italy.},
DOI = {10.4401/ag-8790},
Article-Number = {DM318},
ISSN = {1593-5213},
EISSN = {2037-416X},
Keywords = {Multi Scale Laboratories; Thematic Core Services; EPOS; MSL Subdomain},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {kirsten.elger@gfz-potsdam.de},
Affiliations = {Helmholtz Association; Helmholtz-Center Potsdam GFZ German Research
   Center for Geosciences; Utrecht University; Laboratorio Nacional de
   Energia e Geologia IP (LNEG); University of Munich; Consiglio Nazionale
   delle Ricerche (CNR); Istituto di Geologia Ambientale e Geoingegneria
   (IGAG-CNR); Sapienza University Rome; Universite de Montpellier; Roma
   Tre University; Utrecht University; UK Research \& Innovation (UKRI);
   Natural Environment Research Council (NERC); NERC British Geological
   Survey; Istituto Nazionale Geofisica e Vulcanologia (INGV)},
ResearcherID-Numbers = {Caldeira, Rita/C-8877-2012
   Rosenau, Matthias/I-2081-2016
   Dominguez, Stephane/C-5240-2011
   },
ORCID-Numbers = {Caldeira, Rita/0000-0002-4379-1311
   Rosenau, Matthias/0000-0003-1134-5381
   Dominguez, Stephane/0000-0001-8218-7144
   Lange, Otto/0000-0003-3560-988X
   Wessels, Richard/0000-0003-0714-8705
   FUNICIELLO, Francesca/0000-0001-7900-8272
   Elger, Kirsten/0000-0001-5140-8602},
Number-of-Cited-References = {17},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Ann. Geophys.},
Doc-Delivery-Number = {3I8WF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000832988800005},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000419419200034,
Author = {Schober, Daniel and Jacob, Daniel and Wilson, Michael and Cruz, Joseph
   A. and Marcu, Ana and Grant, Jason R. and Moing, Annick and Deborde,
   Catherine and de Figueiredo, Luis F. and Haug, Kenneth and Rocca-Serra,
   Philippe and Easton, John and Ebbels, Timothy M. D. and Hao, Jie and
   Ludwig, Christian and Guenther, Ulrich L. and Rosato, Antonio and Klein,
   Matthias S. and Lewis, Ian A. and Luchinat, Claudio and Jones, Andrew R.
   and Grauslys, Arturas and Larralde, Martin and Yokochi, Masashi and
   Kobayashi, Naohiro and Porzel, Andrea and Griffin, Julian L. and Viant,
   Mark R. and Wishart, David S. and Steinbeck, Christoph and Salek, Reza
   M. and Neumann, Steffen},
Title = {nmrML: A Community Supported Open Data Standard for the Description,
   Storage, and Exchange of NMR Data},
Journal = {ANALYTICAL CHEMISTRY},
Year = {2018},
Volume = {90},
Number = {1},
Pages = {649-656},
Month = {JAN 2},
Abstract = {NMR is a widely used analytical technique with a growing number of
   repositories available. As a result, demands for a vendor-agnostic, open
   data format for long-term archiving of NMR data have emerged with the
   aim to ease and encourage sharing, comparison, and reuse of NMR data.
   Here we present nmrML, an open XML-based exchange and storage format for
   NMR spectral data. The nmrML format is intended to be fully compatible
   with existing NMR data for chemical, biochemical, and metabolomics
   experiments. nmrML can capture raw NMR data, spectral data acquisition
   parameters, and where available spectral metadata, such as chemical
   structures associated with spectral assignments. The nmrML format is
   compatible with pure-compound NMR data for reference spectral libraries
   as well as NMR data from complex biomixtures, i.e., metabolomics
   experiments. To facilitate format conversions, we provide nmrML
   converters for Bruker, JEOL and Agilent/Varian vendor formats. In
   addition, easy to-use Web-based spectral viewing, processing, and
   spectral assignment tools that read and write nmrML have been developed.
   Software libraries and Web services for data validation are available
   for tool developers and end-users. The nmrML format has already been
   adopted for capturing and disseminating NMR data for small molecules by
   several open source data processing tools and metabolomics reference
   spectral libraries, e.g., serving as storage format for the MetaboLights
   data repository. The nmrML open access data standard has been endorsed
   by the Metabolomics Standards Initiative (MSI), and we here encourage
   user participation and feedback to increase usability and make it a
   successful standard.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Schober, D (Corresponding Author), Leibniz Inst Plant Biochem, Dept Stress \& Dev Biol, Weinberg 3, D-06120 Halle, Germany.
   Salek, RM (Corresponding Author), European Mol Biol Lab, European Bioinformat Inst, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Schober, Daniel; Neumann, Steffen, Leibniz Inst Plant Biochem, Dept Stress \& Dev Biol, Weinberg 3, D-06120 Halle, Germany.
   Jacob, Daniel; Moing, Annick; Deborde, Catherine, Univ Bordeaux, Fruit Biol \& Pathol UMR1332, Bordeaux Funct Genom Ctr, MetaboHUB,IBVM,Ctr INRA Bordeaux,INRA,Metabolome, 71 Av Edouard Bourlaux, F-33140 Villenave Dornon, France.
   Wilson, Michael; Cruz, Joseph A.; Marcu, Ana; Grant, Jason R.; Wishart, David S., Univ Alberta, Dept Comp Sci, Edmonton, AB T6G 2E8, Canada.
   Wilson, Michael; Cruz, Joseph A.; Marcu, Ana; Grant, Jason R.; Wishart, David S., Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E8, Canada.
   de Figueiredo, Luis F.; Haug, Kenneth; Steinbeck, Christoph; Salek, Reza M., European Mol Biol Lab, European Bioinformat Inst, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Rocca-Serra, Philippe, Univ Oxford, E Res Ctr1, 7 Keble Rd, Oxford OX1 3QG, England.
   Easton, John, Univ Birmingham, Sch Engn, Birmingham B15 2TT, W Midlands, England.
   Ebbels, Timothy M. D.; Hao, Jie, Imperial Coll London, Dept Surg \& Canc, Computat \& Syst Med, London SW7 2AZ, England.
   Ludwig, Christian, Univ Birmingham, Inst Metab \& Syst Res, Birmingham B15 2TT, W Midlands, England.
   Guenther, Ulrich L., Univ Birmingham, Inst Canc \& Genom Sci, Birmingham B15 2TT, W Midlands, England.
   Rosato, Antonio; Luchinat, Claudio, Univ Florence, Magnet Resonance Ctr CERM, I-50019 Florence, Italy.
   Rosato, Antonio; Luchinat, Claudio, Univ Florence, Dept Chem, I-50019 Florence, Italy.
   Klein, Matthias S.; Lewis, Ian A., Univ Calgary, Dept Biol Sci, 2500 Univ Dr NW, Calgary, AB T2N 1N4, Canada.
   Jones, Andrew R.; Grauslys, Arturas, Univ Liverpool, Inst Integrat Biol, Biosci Bldg,Crown St, Liverpool L69 7ZB, Merseyside, England.
   Larralde, Martin, Ecole Normale Super Paris Saclay, 61 Ave President Wilson, F-94230 Cachan, France.
   Yokochi, Masashi; Kobayashi, Naohiro, Osaka Univ, IPR, 3-2 Yamadaoka, Suita, Osaka 5650871, Japan.
   Porzel, Andrea, Leibniz Inst Plant Biochem, Dept Bioorgan Chem, D-06120 Halle, Saale, Germany.
   Griffin, Julian L., Univ Cambridge, Dept Biochem, Downing Site, Cambridge CB2 1QW, England.
   Viant, Mark R., Univ Birmingham, Sch Biosci, Birmingham B15 2TT, W Midlands, England.},
DOI = {10.1021/acs.analchem.7b02795},
ISSN = {0003-2700},
EISSN = {1520-6882},
Keywords-Plus = {OPEN SOURCE SOFTWARE; METABOLITE STANDARDS; METABOLOMICS; SPECTRA;
   REPOSITORY; ONTOLOGY; ACCESS},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Analytical},
Author-Email = {dschober@ipb-halle.de
   reza.salek@ebi.ac.uk},
Affiliations = {Leibniz Institut fur Pflanzenbiochemie; INRAE; Universite de Bordeaux;
   University of Alberta; University of Alberta; European Molecular Biology
   Laboratory (EMBL); Wellcome Trust Sanger Institute; University of
   Oxford; University of Birmingham; Imperial College London; University of
   Birmingham; University of Birmingham; University of Florence; University
   of Florence; University of Calgary; University of Liverpool; Universite
   Paris Saclay; Osaka University; Leibniz Institut fur Pflanzenbiochemie;
   University of Cambridge; University of Birmingham},
ResearcherID-Numbers = {Larralde, Martin/JJF-7440-2023
   de Figueiredo, Luis F./R-1204-2019
   Steinbeck, Christoph/B-4131-2008
   Deborde, Catherine/X-6991-2019
   Haug, Ove Kenneth/O-3809-2019
   Deborde, Catherine/AAE-2776-2019
   Hao, Jie/IXW-8033-2023
   Ebbels, Tim/ABB-2627-2021
   Viant, Mark R/B-6339-2009
   Rosato, Antonio/D-8548-2011
   Grant, Jason R/HLG-3620-2023
   Wishart, David Scott/ABI-3181-2020
   Salek, Reza/V-9739-2017
   Easton, John/I-3286-2019
   Haug, Kenneth/AAD-4241-2019
   Deborde, Catherine/HCH-3128-2022
   Klein, Matthias S/H-6893-2013
   Moing, Annick/X-3694-2019
   Neumann, Steffen/K-5554-2012
   Ludwig, Christian/E-7679-2011
   Rosato, Antonio/M-3250-2019
   Jacob, Daniel/AAQ-9846-2020
   Deborde, Catherine/B-6902-2008
   Klein, Matthias S./AAD-6495-2021
   Haug, Ove Kenneth/D-8694-2017
   },
ORCID-Numbers = {Larralde, Martin/0000-0002-3947-4444
   Deborde, Catherine/0000-0001-5687-9059
   Deborde, Catherine/0000-0001-5687-9059
   Hao, Jie/0000-0002-0273-8047
   Ebbels, Tim/0000-0002-3372-8423
   Viant, Mark R/0000-0001-5898-4119
   Rosato, Antonio/0000-0001-6172-0368
   Salek, Reza/0000-0001-8604-1732
   Easton, John/0000-0001-8745-6753
   Deborde, Catherine/0000-0001-5687-9059
   Klein, Matthias S/0000-0001-7455-5381
   Moing, Annick/0000-0003-1144-3600
   Neumann, Steffen/0000-0002-7899-7192
   Ludwig, Christian/0000-0001-8901-6970
   Rosato, Antonio/0000-0001-6172-0368
   Jacob, Daniel/0000-0002-6687-7169
   Deborde, Catherine/0000-0001-5687-9059
   Klein, Matthias S./0000-0001-7455-5381
   Jones, Andrew/0000-0001-6118-9327
   Gunther, Ulrich/0000-0001-9840-5943
   Lewis, Ian A./0000-0002-5753-499X
   Schober, Daniel/0000-0001-8014-6648
   Haug, Ove Kenneth/0000-0003-3168-4145
   Grauslys, Arturas/0000-0002-6736-6854
   Steinbeck, Christoph/0000-0001-6966-0814},
Funding-Acknowledgement = {EU FP7 Project COSMOS Grant {[}EC312941]; Genome Canada; Canadian
   Institutes of Health Research; Alberta Innovates Health Solutions (AIRS,
   Translational Health Chair); Natural Sciences and Engineering Research
   Council (NSERC) {[}04547]; MetaboHUB {[}ANR-11-INBS-0010]; UK's
   Biotechnology and Biological Sciences Research Council (BBSRC)
   {[}BB/M020282/1]; BBSRC {[}BB/M027635/1, BB/M019985/1]; MRC UK MEDical
   BIOinformatics partnership {[}MR/L01632X/1]; PhenoMeNal European
   Commission's Horizon program {[}654241]; BBSRC {[}BB/M027635/1,
   BB/M020282/1, BB/L024152/1, BB/M019985/1, BB/D01638X/1] Funding Source:
   UKRI; MRC {[}MC\_UP\_A090\_1006, MR/P011705/1, MR/L01632X/1] Funding
   Source: UKRI; Alberta Innovates {[}201201143, 201401122] Funding Source:
   researchfish; Biotechnology and Biological Sciences Research Council
   {[}BB/M019985/1, BB/L024152/1, BB/M027635/1, BB/M020282/1, BB/D01638X/1]
   Funding Source: researchfish; Medical Research Council
   {[}MC\_UP\_A090\_1006, MR/P011705/1, MR/L01632X/1] Funding Source:
   researchfish; Grants-in-Aid for Scientific Research {[}15K06970] Funding
   Source: KAKEN},
Funding-Text = {This work was financed via the EU FP7 Project COSMOS Grant EC312941,
   Genome Canada and the Canadian Institutes of Health Research. I.A.L. and
   M.S.K. (rNMR) are supported by Alberta Innovates Health Solutions (AIRS,
   Translational Health Chair) and the Natural Sciences and Engineering
   Research Council (NSERC, Discovery Grant 04547). DJ., A. Moing, and C.D.
   thank MetaboHUB ANR-11-INBS-0010 for financing. A.RJ. and A.G.
   acknowledge funding from the UK's Biotechnology and Biological Sciences
   Research Council (BBSRC) Grant BB/M020282/1. R.M.S. acknowledges BBSRC
   Grant BB/M027635/1 and MRC UK MEDical BIOinformatics partnership, Grant
   MR/L01632X/1. M.R.V. acknowledges BBSRC Grant BB/M019985/1, D.S., C.S,
   S.N., P.R-S., and R.M.S. acknowledge the PhenoMeNal European
   Commission's Horizon2020 program, Grant 654241. We thank the late Ivano
   Bertini for his initial vision towards this standardization effort. The
   nmrML logo is copyrighted by nmrML.org.},
Number-of-Cited-References = {36},
Times-Cited = {36},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {32},
Journal-ISO = {Anal. Chem.},
Doc-Delivery-Number = {FR9US},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000419419200034},
OA = {Green Submitted, Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000525956700096,
Author = {Bogue, Molly A. and Philip, Vivek M. and Walton, David O. and Grubb,
   Stephen C. and Dunn, Matthew H. and Kolishovski, Georgi and Emerson,
   Jake and Mukherjee, Gaurab and Stearns, Timothy and He, Hao and Sinha,
   Vinita and Kadakkuzha, Beena and Kunde-Ramamoorthy, Govindarajan and
   Chesler, Elissa J.},
Title = {Mouse Phenome Database: a data repository and analysis suite for curated
   primary mouse phenotype data},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2020},
Volume = {48},
Number = {D1},
Pages = {D716-D723},
Month = {JAN 8},
Abstract = {The Mouse Phenome Database (MPD; https://phenome.jax.org) is a widely
   accessed and highly functional data repository housing primary phenotype
   data for the laboratory mouse accessible via APIs and providing tools to
   analyze and visualize those data. Data come from investigators around
   the world and represent a broad scope of phenotyping endpoints and
   disease-related traits in naive mice and those exposed to drugs,
   environmental agents or other treatments. MPD houses rigorously curated
   per-animal data with detailed protocols. Public ontologies and
   controlled vocabularies are used for annotation. In addition to
   phenotype tools, genetic analysis tools enable users to integrate and
   interpret genome-phenome relations across the database. Strain types and
   populations include inbred, recombinant inbred, F1 hybrid, transgenic,
   targeted mutants, chromosome substitution, Collaborative Cross,
   Diversity Outbred and other mapping populations. Our new analysis tools
   allow users to apply selected data in an integrated fashion to address
   problems in trait associations, reproducibility, polygenic syndrome
   model selection and multi-trait modeling. As we refine these tools and
   approaches, we will continue to provide users a means to identify
   consistent, quality studies that have high translational relevance.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bogue, MA (Corresponding Author), Jackson Lab, Bar Harbor, ME 04609 USA.
   Bogue, Molly A.; Philip, Vivek M.; Walton, David O.; Grubb, Stephen C.; Dunn, Matthew H.; Kolishovski, Georgi; Emerson, Jake; Mukherjee, Gaurab; Stearns, Timothy; He, Hao; Sinha, Vinita; Kadakkuzha, Beena; Kunde-Ramamoorthy, Govindarajan; Chesler, Elissa J., Jackson Lab, Bar Harbor, ME 04609 USA.},
DOI = {10.1093/nar/gkz1032},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {COLLABORATIVE CROSS; BEHAVIOR},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {molly.bogue@jax.org},
Affiliations = {Jackson Laboratory},
ResearcherID-Numbers = {Chesler, Elissa/K-4641-2019
   },
ORCID-Numbers = {Chesler, Elissa/0000-0002-5642-5062
   Walton, David/0000-0002-9848-6808
   Philip, Vivek/0000-0001-5126-707X
   Stearns, Timothy/0000-0002-5533-6076
   Emerson, Jake/0000-0003-0617-9219},
Funding-Acknowledgement = {National Institute on Drug Abuse, National Institutes of Health
   {[}DA028420, DA045401]; National Institute on Aging, National Institutes
   of Health {[}AG022308, AG066346]; National Institutes of Health
   {[}DA028420]},
Funding-Text = {National Institute on Drug Abuse, National Institutes of Health
   {[}DA028420, DA045401]; National Institute on Aging, National Institutes
   of Health {[}AG022308, AG066346]. Funding for open access charge:
   National Institutes of Health {[}DA028420].},
Number-of-Cited-References = {17},
Times-Cited = {42},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {LD3UB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000525956700096},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000878619400001,
Author = {Bogue, Molly A. and Ball, Robyn L. and Philip, Vivek M. and Walton,
   David O. and Dunn, Matthew H. and Kolishovski, Georgi and Lamoureux,
   Anna and Gerring, Matthew and Liang, Hongping and Emerson, Jake and
   Stearns, Tim and He, Hao and Mukherjee, Gaurab and Bluis, John and
   Desai, Sejal and Sundberg, Beth and Kadakkuzha, Beena and
   Kunde-Ramamoorthy, Govindarajan and Chesler, Elissa J.},
Title = {Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy
   data repository and tool suite for phenotypes and genotypes},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2023},
Volume = {51},
Number = {D1},
Pages = {D1067-D1074},
Month = {JAN 6},
Abstract = {The Mouse Phenome Database (MPD; https://phenome.jax.org;
   RRID:SCR\_003212), supported by the US National Institutes of Health, is
   a Biomedical Data Repository listed in the Trans-NIH Biomedical
   Informatics Coordinating Committee registry. As an increasingly
   FAIR-compliant and TRUST-worthy data repository, MPD accepts phenotype
   and genotype data from mouse experiments and curates, organizes,
   integrates, archives, and distributes those data using community
   standards. Data are accompanied by rich metadata, including widely used
   ontologies and detailed protocols. Data are from all over the world and
   represent genetic, behavioral, morphological, and physiological
   disease-related characteristics in mice at baseline or those exposed to
   drugs or other treatments. MPD houses data from over 6000 strains and
   populations, representing many reproducible strain types and
   heterogenous populations such as the Diversity Outbred where each mouse
   is unique but can be genotyped throughout the genome. A suite of
   analysis tools is available to aggregate, visualize, and analyze these
   data within and across studies and populations in an increasingly
   traceable and reproducible manner. We have refined existing resources
   and developed new tools to continue to provide users with access to
   consistent, high-quality data that has translational relevance in a
   modernized infrastructure that enables interaction with a suite of
   bioinformatics analytic and data services.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bogue, MA (Corresponding Author), Jackson Lab, Bar Harbor, ME 04609 USA.
   Bogue, Molly A.; Ball, Robyn L.; Philip, Vivek M.; Walton, David O.; Dunn, Matthew H.; Kolishovski, Georgi; Lamoureux, Anna; Gerring, Matthew; Liang, Hongping; Emerson, Jake; Stearns, Tim; He, Hao; Mukherjee, Gaurab; Bluis, John; Desai, Sejal; Sundberg, Beth; Kadakkuzha, Beena; Kunde-Ramamoorthy, Govindarajan; Chesler, Elissa J., Jackson Lab, Bar Harbor, ME 04609 USA.},
DOI = {10.1093/nar/gkac1007},
EarlyAccessDate = {NOV 2022},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {DIVERSITY; GENOME; CROSS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {molly.bogue@jax.org},
Affiliations = {Jackson Laboratory},
ResearcherID-Numbers = {Chesler, Elissa/K-4641-2019
   },
ORCID-Numbers = {Chesler, Elissa/0000-0002-5642-5062
   Mukherjee, Gaurab/0000-0002-1473-4174
   Bogue, Molly/0000-0001-6624-9261
   Lamoureux, Anna/0009-0003-9460-1367
   Walton, David/0000-0002-9848-6808
   Emerson, Jake/0000-0003-0617-9219},
Funding-Acknowledgement = {National Institutes of Health {[}DA028420, AG066346, DA039841,
   OD030187]; Jackson Laboratory Director's Innovation Fund; Cube
   Initiative; National Institutes of Health, NIDA},
Funding-Text = {National Institutes of Health {[}DA028420, AG066346 to M.A.B., DA039841,
   OD030187 to E.J.C. andR.L.B.]; Jackson Laboratory Director's Innovation
   Fund and Cube Initiative. Funding for open access charge: National
   Institutes of Health, NIDA.},
Number-of-Cited-References = {26},
Times-Cited = {4},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {Q5NY7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000878619400001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000316180000001,
Author = {Pan, Huaqin and Ardini, Mary-Anne and Bakalov, Vesselina and DeLatte,
   Michael and Eggers, Paul and Ganapathi, Laxminarayana and Hollingsworth,
   Craig R. and Levy, Joshua and Li, Sheping and Pratt, Joseph and Pugh,
   Norma and Qin, Ying and Rasooly, Rebekah and Ray, Helen and Richardson,
   Jean E. and Riley, Amanda Flynn and Rogers, Susan M. and Tan, Sylvia and
   Turner, Charles F. and White, Stacie and Cooley, Philip C.},
Title = {`What's in the NIDDK CDR?'-public query tools for the NIDDK central data
   repository},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2013},
Month = {FEB 8},
Abstract = {The National Institute of Diabetes and Digestive Disease (NIDDK) Central
   Data Repository (CDR) is a web-enabled resource available to researchers
   and the general public. The CDR warehouses clinical data and study
   documentation from NIDDK funded research, including such landmark
   studies as The Diabetes Control and Complications Trial (DCCT, 1983-93)
   and the Epidemiology of Diabetes Interventions and Complications (EDIC,
   1994-present) follow-up study which has been ongoing for more than 20
   years. The CDR also houses data from over 7 million biospecimens
   representing 2 million subjects. To help users explore the vast amount
   of data stored in the NIDDK CDR, we developed a suite of search
   mechanisms called the public query tools (PQTs). Five individual tools
   are available to search data from multiple perspectives: study search,
   basic search, ontology search, variable summary and sample by condition.
   PQT enables users to search for information across studies. Users can
   search for data such as number of subjects, types of biospecimens and
   disease outcome variables without prior knowledge of the individual
   studies. This suite of tools will increase the use and maximize the
   value of the NIDDK data and biospecimen repositories as important
   resources for the research community. Database
   URL:https://www.niddkrepository.org/niddk/home.do},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Cooley, PC (Corresponding Author), RTI Int Social Stat \& Environm Sci, POB 12194, Res Triangle Pk, NC 27709 USA.
   Pan, Huaqin; Ardini, Mary-Anne; Bakalov, Vesselina; DeLatte, Michael; Ganapathi, Laxminarayana; Hollingsworth, Craig R.; Levy, Joshua; Li, Sheping; Pratt, Joseph; Pugh, Norma; Qin, Ying; Ray, Helen; Richardson, Jean E.; Riley, Amanda Flynn; Rogers, Susan M.; Tan, Sylvia; Turner, Charles F.; White, Stacie; Cooley, Philip C., RTI Int Social Stat \& Environm Sci, Res Triangle Pk, NC 27709 USA.
   Eggers, Paul; Rasooly, Rebekah, NIDDK, Div Kidney Urol \& Hematol Dis, Bethesda, MD 20892 USA.
   Turner, Charles F., CUNY Queens Coll, Flushing, NY 11367 USA.
   Turner, Charles F., CUNY Grad Ctr, Flushing, NY 11367 USA.},
DOI = {10.1093/database/bas058},
Article-Number = {bas058},
ISSN = {1758-0463},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {pcc@rtii.org},
Affiliations = {Research Triangle Institute; National Institutes of Health (NIH) - USA;
   NIH National Institute of Diabetes \& Digestive \& Kidney Diseases
   (NIDDK); City University of New York (CUNY) System; Queens College NY
   (CUNY); City University of New York (CUNY) System; City University of
   New York (CUNY) Graduate School},
ORCID-Numbers = {Savage, Helen/0000-0002-5111-576X
   Pugh, Norma/0000-0003-3052-2232
   Qin, Ying/0000-0002-6099-2190
   Pan, Huaqin/0000-0002-7166-108X
   Rasooly, Rebekah/0000-0002-6357-5528
   Ardini-Poleske, Maryanne/0000-0001-7622-026X
   Tan, Sylvia Margaret/0000-0002-2987-0072
   Ganapathi, Laxminarayana/0000-0001-8751-3797},
Funding-Acknowledgement = { {[}HHSN267200800016C]},
Funding-Text = {National Institute of Diabetes and Digestive and Kidney Diseases;
   National Institutes of Health, NIH American Recovery and Reinvestment
   Act (ARRA) of 2009, Department of Health and Human Services, under
   Contracts (HHSN: 267200800015C, 267200800016C and 267200800018C).
   Funding for open access charge: HHSN267200800016C.},
Number-of-Cited-References = {5},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Database},
Doc-Delivery-Number = {106XZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000316180000001},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000481972100020,
Author = {Vela, Belen and Maria Cavero, Jose and Caceres, Paloma and Cuesta,
   Carlos E.},
Title = {A Semi-Automatic Data-Scraping Method for the Public Transport Domain},
Journal = {IEEE ACCESS},
Year = {2019},
Volume = {7},
Pages = {105627-105637},
Abstract = {The growing amount of data on the Internet has led to a situation in
   which it is essential to process these data to generate new services
   with the specific aim of improving people's daily living conditions.
   Transport data is of the utmost importance, since everyday people have
   to move around to perform some daily tasks, such as going to work,
   studying and shopping, and this means that the number of journeys by
   public transport grows daily. People with special needs make a large
   number of these trips, but they do not have sufficient information about
   the accessibility of the routes they want to take. Although there are
   numerous websites and applications that provide information on public
   transport services, most do not provide detailed information on the
   accessibility of the routes. We are, therefore, developing a
   technological framework for the processing, management, and exploitation
   of open data to promote accessibility to urban public transport. This is
   taking place within the framework of the Access@City project. This paper
   specifically focuses on the data extraction and processing of the
   existing information on the web concerning public transport and its
   accessibility for the generation of an open data repository in which to
   store this information. We, therefore, propose a method for the
   semi-automatic generation of a data scraper for the public transport
   domain. This method allows the extraction of public transport data and
   the existing accessibility information from a selected website. We have
   additionally developed a web tool that employs the aforementioned method
   to generate a data scraper for the public transport domain.},
Publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC},
Address = {445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA},
Type = {Article},
Language = {English},
Affiliation = {Vela, B (Corresponding Author), Rey Juan Carlos Univ, Dept Comp Sci \& Stat, Madrid 28933, Spain.
   Vela, Belen; Maria Cavero, Jose; Caceres, Paloma; Cuesta, Carlos E., Rey Juan Carlos Univ, Dept Comp Sci \& Stat, Madrid 28933, Spain.},
DOI = {10.1109/ACCESS.2019.2932197},
ISSN = {2169-3536},
Keywords = {Accessibility; code generation; open data; public transport; smart city;
   web scraping},
Keywords-Plus = {WEB DATA EXTRACTION; INFORMATION},
Research-Areas = {Computer Science; Engineering; Telecommunications},
Web-of-Science-Categories  = {Computer Science, Information Systems; Engineering, Electrical \&
   Electronic; Telecommunications},
Author-Email = {belen.vela@urjc.es},
Affiliations = {Universidad Rey Juan Carlos},
ResearcherID-Numbers = {de Marina, Paloma Cáceres García/K-7559-2012
   Cavero, Jose Maria/K-5372-2012
   Cuesta, Carlos/B-4902-2012
   Sanchez, Belen Vela/H-1561-2015},
ORCID-Numbers = {de Marina, Paloma Cáceres García/0000-0002-2722-2434
   Cavero, Jose Maria/0000-0001-5324-1383
   Cuesta, Carlos/0000-0003-0286-4219
   Sanchez, Belen Vela/0000-0003-0604-7312},
Funding-Acknowledgement = {Spanish Ministry of Science, Innovation and Universities
   {[}TIN2016-78103-C2-1-R]},
Funding-Text = {This work was supported in part by the Access@City Research Project
   TIN2016-78103-C2-1-R, funded by the Spanish Ministry of Science,
   Innovation and Universities.},
Number-of-Cited-References = {23},
Times-Cited = {4},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {IEEE Access},
Doc-Delivery-Number = {IS2GX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000481972100020},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000893771100001,
Author = {Hoch, Jeffrey C. and Baskaran, Kumaran and Burr, Harrison and Chin, John
   and Eghbalnia, Hamid R. and Fujiwara, Toshimichi and Gryk, Michael R.
   and Iwata, Takeshi and Kojima, Chojiro and Kurisu, Genji and Maziuk,
   Dmitri and Miyanoiri, Yohei and Wedell, Jonathan R. and Wilburn, Colin
   and Yao, Hongyang and Yokochi, Masashi},
Title = {Biological Magnetic Resonance Data Bank},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2023},
Volume = {51},
Number = {D1},
Pages = {D368-D376},
Month = {JAN 6},
Abstract = {The Biological Magnetic Resonance Data Bank (BMRB, ) is the
   international open data repository for biomolecular nuclear magnetic
   resonance (NMR) data. Comprised of both empirical and derived data, BMRB
   has applications in the study of biomacromolecular structure and
   dynamics, biomolecular interactions, drug discovery, intrinsically
   disordered proteins, natural products, biomarkers, and metabolomics.
   Advances including GHz-class NMR instruments, national and
   trans-national NMR cyberinfrastructure, hybrid structural biology
   methods and machine learning are driving increases in the amount, type,
   and applications of NMR data in the biosciences. BMRB is a Core Archive
   and member of the World-wide Protein Data Bank (wwPDB).},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Hoch, JC (Corresponding Author), UConn Hlth, Dept Mol Biol \& Biophys, Farmington, CT 06030 USA.
   Hoch, Jeffrey C.; Baskaran, Kumaran; Burr, Harrison; Chin, John; Eghbalnia, Hamid R.; Gryk, Michael R.; Maziuk, Dmitri; Wedell, Jonathan R.; Wilburn, Colin; Yao, Hongyang, UConn Hlth, Dept Mol Biol \& Biophys, Farmington, CT 06030 USA.
   Fujiwara, Toshimichi; Iwata, Takeshi; Kojima, Chojiro; Kurisu, Genji; Miyanoiri, Yohei; Yokochi, Masashi, Osaka Univ, Inst Prot Res, Prot Data Bank Japan, Suita, Osaka 5650871, Japan.
   Kojima, Chojiro, Yokohama Natl Univ, Grad Sch Engn Sci, Yokohama 2408501, Japan.},
DOI = {10.1093/nar/gkac1050},
EarlyAccessDate = {DEC 2022},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PROTEIN-STRUCTURE DETERMINATION; NMR CHEMICAL-SHIFT; MACROMOLECULAR
   STRUCTURES; STAR FILE; PREDICTION; RESOURCE; FORMAT; SYSTEM; TOOLS;
   WWPDB},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {hoch@uchc.edu},
Affiliations = {Osaka University; Yokohama National University},
ResearcherID-Numbers = {KURISU, GENJI/ABA-5960-2020
   },
ORCID-Numbers = {KURISU, GENJI/0000-0002-5354-0807
   Hoch, Jeffrey/0000-0002-9230-2019},
Funding-Acknowledgement = {US National Institutes ofHealth; Database Integration Coordination
   Program fromthe department of NBDC program, Japan Science andTechnology
   Agency {[}R01GM109046]; Platform Project forSupporting Drug Discovery
   and Life Science Research (Ba-sis for Supporting Innovative Drug
   Discovery and Life Sci-ence Research (BINDS)) from AMED {[}JPMJND2205];
   Hoch discretionary funds {[}22ama121001]},
Funding-Text = {B.M.R.B. is supported by the US National Institutes ofHealth
   {[}R01GM109046]; BMRBj was supported by grantsfrom the Database
   Integration Coordination Program fromthe department of NBDC program,
   Japan Science andTechnology Agency {[}JPMJND2205]; Platform Project
   forSupporting Drug Discovery and Life Science Research (Ba-sis for
   Supporting Innovative Drug Discovery and Life Sci-ence Research (BINDS))
   from AMED {[}22ama121001, inpart] Funding for open access charge: Hoch
   discretionary funds},
Number-of-Cited-References = {48},
Times-Cited = {29},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {Q5NY7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000893771100001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001047820400001,
Author = {Alindayu, Ricardo C. and Licnachan, Lance Oliver C. and Luzadas, Ramgem
   L. and Ignacio, Paul Samuel P. and Onda, Deo Florence L.},
Title = {Moving towards open data, public access, and information sharing to
   combat marine plastics pollution in the Philippines and the Southeast
   Asian region},
Journal = {OCEAN \& COASTAL MANAGEMENT},
Year = {2023},
Volume = {243},
Month = {SEP 1},
Abstract = {ABS T R A C T Despite the consistent tagging of countries in Southeast
   Asia as among the top polluters of plastics in the oceans and the
   increasing local literature documenting the presence and abundance of
   plastics in marine environments, there still lacks a comprehensive,
   open, and accessible repository for marine plastics pollution data in
   the region. As such, this study presents the development of the
   PlastiCount Pilipinas portal in line with the call for a common data
   repository by the Philippines' National Plan of Action for the
   Prevention, Reduction, and Management of Marine Litter and the ASEAN
   Regional Action Plan for Combating Marine Debris in the ASEAN Member
   States. A total of 14 existing databases were reviewed to identify key
   features for the online portal implemented to pro-mote ease of access
   and diversified functionality. For the database, a total of 38
   publications, 2 reports, 1 sci-entific poster, and 3 baselining studies
   were used to develop the initial ground-truthed baseline for marine
   plastic pollution, covering 23 provinces and 14 regions across the
   Philippines. The challenges presented by an observed variation across
   different methodologies and reporting styles emphasize the critical need
   to harmonize methods toward generating a more refined national baseline
   for marine litter. The initial baseline data and other resources such as
   manuals, information sheets, photographs, news, and publications are
   uploaded onto a public online portal for viewing and download
   (https://plasticount.ph/). Data and resource submissions from the public
   are also accepted and considered for inclusion in the database. The
   insights gained from developing the online portal and database for the
   Philippines can be used to inform the development of a regional database
   for Southeast Asia towards reducing marine litter.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Onda, DFL (Corresponding Author), Univ Philippines, Marine Sci Inst, Microbial Oceanog Lab, Room 201,Velasquez St, Quezon City 1101, Diliman, Philippines.
   Alindayu, Ricardo C.; Luzadas, Ramgem L.; Onda, Deo Florence L., Univ Philippines, Marine Sci Inst, Microbial Oceanog Lab, Quezon City 1101, Diliman, Philippines.
   Licnachan, Lance Oliver C.; Ignacio, Paul Samuel P., Univ Philippines Baguio, Dept Math \& Comp Sci, Gov Pack Rd, Baguio 2600, Philippines.
   Onda, Deo Florence L., Univ Philippines, Marine Sci Inst, Microbial Oceanog Lab, Room 201,Velasquez St, Quezon City 1101, Diliman, Philippines.},
DOI = {10.1016/j.ocecoaman.2023.106771},
EarlyAccessDate = {JUL 2023},
Article-Number = {106771},
ISSN = {0964-5691},
EISSN = {1873-524X},
Keywords = {Plastic pollution; National database; Marine debris; Monitoring; Open
   data},
Keywords-Plus = {LITTER; BEACH; ABUNDANCE},
Research-Areas = {Oceanography; Water Resources},
Web-of-Science-Categories  = {Oceanography; Water Resources},
Author-Email = {dfonda@msi.upd.edu.ph},
Affiliations = {University of the Philippines System; University of the Philippines
   Diliman; University of the Philippines System; University of the
   Philippines Baguio; University of the Philippines System; University of
   the Philippines Diliman},
ResearcherID-Numbers = {IGNACIO, PAUL SAMUEL/AAH-2627-2019},
ORCID-Numbers = {IGNACIO, PAUL SAMUEL/0000-0002-0712-0414},
Funding-Acknowledgement = {JST-UKRI-DOST Science and Technology and Action Nexus for Development;
   JST-UKRI-DOST Science and Technology and Action Nexus for Development
   (STAND); DOST-Philippine Council for Industry, Energy, and Emerging
   Technology Research and Development (DOST-PCIEERD) {[}9861]; Department
   of Science and Technology - National Research Council of the Philippines
   (DOST-NRCP); United Kingdom Research and Innovation (UKRI); National
   Security Council (NSC); Department of Environment and Natural Resources
   Biodiversity Management Bureau (DENR-BMB)},
Funding-Text = {The authors would like to acknowledge the support extended through the
   JST-UKRI-DOST Science and Technology and Action Nexus for Development
   (STAND) -funded and DOST-Philippine Council for Industry, Energy, and
   Emerging Technology Research and Development (DOST-PCIEERD) -monitored
   ``PlastiCount Pilipinas: Counting and Visualizing Marine Plastics
   Pollution in the Philippines{''} (Project No. 9861) . Additionally, the
   authors would like to acknowledge the Department of Science and
   Technology - National Research Council of the Philippines (DOST-NRCP)
   -funded ``Plastics in the marine environment, trophic sys-tems, and
   aquaculture (PlasMics) `` project, the United Kingdom Research and
   Innovation (UKRI) -funded ``Microbial Transformation of Plastics in
   South East Asian Seas: A Hazard and A Solution (MicroSEAP) `` project,
   the National Security Council (NSC) -funded ``Upgrading Capability,
   Infrastructure, and Assets for Marine Scientific Research in the
   Philippines (UPGRADE-CIA) `` project, and the Department of Environment
   and Natural Resources Biodiversity Management Bureau (DENR-BMB) -funded
   ``Predicting Responses between Ocean Transport and Ecological
   Connectivity of Threatened Ecosystems in the West Philippine Sea
   (PROTECT-WPS) `` project for data contributions to the portal. We also
   would like to express our gratitude towards the members of the Microbial
   Oceanography Laboratory of the University of the Philippines, The Marine
   Science Institute, especially Robert Bryan Casauay, Norchel Corcia
   Gomez, Daniel John Purganan, Noe Reyes, and Laurence Insigne for
   providing their data to the web portal. Icons used in this work were
   provided by Freepik on https://flaticon.com /.},
Number-of-Cited-References = {100},
Times-Cited = {5},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Ocean Coastal Manage.},
Doc-Delivery-Number = {P0SI4},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001047820400001},
DA = {2024-01-15},
}

@article{ WOS:000439538900002,
Author = {Ikeuchi, Ui},
Title = {An Analysis of Open Research Data Practice, Drivers, and Barriers in
   Japan},
Journal = {LIBRARY AND INFORMATION SCIENCE},
Year = {2018},
Number = {79},
Pages = {21-57},
Abstract = {{[}Purpose] This study contributes to the development of open science
   policies and appropriate support frameworks by clarifying the status and
   perceptions of open research data, and analyzing drivers and barriers
   among researchers in Japan.
   {[}Methods] From November to December 2016, 1,983 researchers from the
   Science and Technology Experts Network operated by the National
   Institute of Science and Technology Policy took part in a survey. The
   responses were analyzed for participants age and disciplines and
   compared with open access status and previous research results. The
   reasons for and experience with open data were investigated; the
   characteristics of researchers who have open data experience were
   clarified using binomial regression analysis. Reasons for non-disclosure
   of data and degree of barriers to disclosure were investigated. The
   characteristics of fields with high and low open data rates compared
   with the strength of journal open data policies were also clarified.
   {[}Results] Responses were received from 1,398 researchers (70.5\%) who
   belonged to universities, companies, and public
   institutions/organizations. Of the respondents, 51.0\% had experience
   publishing data; the main reason for disclosure was the improvement of
   cognition of research results and journal policies. The reasons for
   non-disclosure varied, including the lack of a journal policy, and only
   28.4\% respondents would publicize their data if the issues were
   resolved. Of the researchers, 75.8\% had obtained published data and
   97.1\% exhibited a willingness to use published data. Respondents
   recognize that there is a lack of human resources, funds, time, and data
   repositories, which are required resources for data publishing. There
   were strong concerns, particularly among younger researchers belonging
   to universities, regarding career risks, such as using data without
   citation or priority loss. There were also strong concerns regarding
   confidentiality, commercial use, and misuse.
   The resulting analysis suggests that important issues for promoting data
   publishing include improving the availability of open research data and
   providing support staff to set aside time for researchers. To solve
   career risk concerns and the lack of incentives, it is important to make
   the publishing of data a recognized research achievement.},
Publisher = {MITA SOC LIBRARY INFORMATION SCIENCE},
Address = {C/O SCH LIB \& INFO SCIENCE, KEIO UNIV 2-15-45 MITA, MINATO-KU, TOKYO,
   108-8345, JAPAN},
Type = {Article},
Language = {Japanese},
Affiliation = {Ikeuchi, U (Corresponding Author), Univ Tsukuba, Grad Sch Lib Informat \& Media Studies, 1-2 Kasuga, Tsukuba, Ibaraki 3058550, Japan.
   Ikeuchi, U (Corresponding Author), Minist Educ Culture Sports Sci \& Technol MEXT, Natl Inst Sci \& Technol Policy NISTEP, 1-2 Kasuga, Tsukuba, Ibaraki 3058550, Japan.
   Ikeuchi, Ui, Univ Tsukuba, Grad Sch Lib Informat \& Media Studies, 1-2 Kasuga, Tsukuba, Ibaraki 3058550, Japan.
   Ikeuchi, Ui, Minist Educ Culture Sports Sci \& Technol MEXT, Natl Inst Sci \& Technol Policy NISTEP, 1-2 Kasuga, Tsukuba, Ibaraki 3058550, Japan.},
ISSN = {0373-4447},
Keywords-Plus = {RESEARCH DATA-MANAGEMENT; BIODIVERSITY DATA; SCIENCES; SHARE; LIBRARIES;
   SERVICES; ACCESS; ROLES; NORMS},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {ikeuchi.ui@gmail.com},
Affiliations = {University of Tsukuba; National Institute of Science \& Technology
   Policy (NISTEP)},
ResearcherID-Numbers = {Ikeuchi, Ui/N-8436-2015},
ORCID-Numbers = {Ikeuchi, Ui/0000-0002-5680-1881},
Number-of-Cited-References = {73},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {38},
Journal-ISO = {Libr. Inf. Sci.},
Doc-Delivery-Number = {GN9QL},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000439538900002},
DA = {2024-01-15},
}

@article{ WOS:000352909400005,
Author = {Weichselbraun, Albert and Streiff, Daniel and Scharl, Arno},
Title = {Consolidating Heterogeneous Enterprise Data for Named Entity Linking and
   Web Intelligence},
Journal = {INTERNATIONAL JOURNAL ON ARTIFICIAL INTELLIGENCE TOOLS},
Year = {2015},
Volume = {24},
Number = {2, SI},
Month = {APR},
Abstract = {Linking named entities to structured knowledge sources paves the way for
   state-of-the-art Web intelligence applications which assign sentiment to
   the correct entities, identify trends, and reveal relations between
   organizations, persons and products. For this purpose this paper
   introduces Recognyze, a named entity linking component that uses
   background knowledge obtained from linked data repositories, and
   outlines the process of transforming heterogeneous data silos within an
   organization into a linked enterprise data repository which draws upon
   popular linked open data vocabularies to foster interoperability with
   public data sets. The presented examples use comprehensive real-world
   data sets from Orell Fussli Business Information, Switzerland's largest
   business information provider. The linked data repository created from
   these data sets comprises more than nine million triples on companies,
   the companies' contact information, key people, products and brands. We
   identify the major challenges of tapping into such sources for named
   entity linking, and describe required data pre-processing techniques to
   use and integrate such data sets, with a special focus on disambiguation
   and ranking algorithms. Finally, we conduct a comprehensive evaluation
   based on business news from the New Journal of Zurich and AWP Financial
   News to illustrate how these techniques improve the performance of the
   Recognyze named entity linking component.},
Publisher = {WORLD SCIENTIFIC PUBL CO PTE LTD},
Address = {5 TOH TUCK LINK, SINGAPORE 596224, SINGAPORE},
Type = {Article},
Language = {English},
Affiliation = {Weichselbraun, A (Corresponding Author), Univ Appl Sci, Swiss Inst Informat Res, Pulvermuhlestr 57, CH-7004 Chur, Switzerland.
   Weichselbraun, Albert; Streiff, Daniel, Univ Appl Sci, Swiss Inst Informat Res, CH-7004 Chur, Switzerland.
   Scharl, Arno, MODUL Univ Vienna, Dept New Media Technol, A-1190 Vienna, Austria.},
DOI = {10.1142/S0218213015400084},
Article-Number = {1540008},
ISSN = {0218-2130},
EISSN = {1793-6349},
Keywords = {linked open data; linked enterprise data; named entity linking; named
   entity resolution; business news; Web intelligence; data pre-processing;
   data consolidation},
Keywords-Plus = {BUSINESS},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Artificial Intelligence; Computer Science,
   Interdisciplinary Applications},
Author-Email = {albert.weichselbraun@htwchur.ch
   daniel.streiff@htwchur.ch
   scharl@modul.ac.at},
ResearcherID-Numbers = {Scharl, Arno/N-3411-2013
   Weichselbraun, Albert/C-3832-2014},
ORCID-Numbers = {Scharl, Arno/0000-0001-5346-9521
   Weichselbraun, Albert/0000-0001-6399-045X},
Funding-Acknowledgement = {Swiss Commission for Technology and Innovation (CTI); DecarboNet project
   (decarbonet.eu) - European Union's 7th Framework Programme for research,
   technology development and demonstration {[}610829]},
Funding-Text = {The research presented in this paper has been conducted as part of the
   COMET Project (www.htwchur.ch/comet), funded by the Swiss Commission for
   Technology and Innovation (CTI), and the DecarboNet project
   (decarbonet.eu), funded by the European Union's 7th Framework Programme
   for research, technology development and demonstration under the Grant
   Agreement No. 610829. The authors would like to thank Max Gobel for
   integrating Recognyze into the Media Watch on Climate Change
   (www.ecoresearch.net/climate).},
Number-of-Cited-References = {34},
Times-Cited = {10},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {18},
Journal-ISO = {Int. J. Artif. Intell. Tools},
Doc-Delivery-Number = {CF9TJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000352909400005},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000558617400006,
Author = {Naujokat, Anke and Glitsch, Tobias and Martin, Felix and Schlimme,
   Hermann},
Title = {BAUREKA.ONLINE - RESEARCH REPOSITORY, CATALOGUE AND ARCHIVE FOR
   ARCHITECTURAL HISTORY AND BUILDING ARCHAEOLOGY},
Journal = {SCIRES-IT-SCIENTIFIC RESEARCH AND INFORMATION TECHNOLOGY},
Year = {2020},
Volume = {10},
Number = {1},
Pages = {43-52},
Abstract = {Building archaeology (Historische Bauforschung) is an internationally
   renowned methodology for investigating historic buildings in research,
   heritage preservation and planning. It is a hands-on process which
   documents the geometry, construction, materiality, usage, form, and
   meaning of buildings and makes it possible to trace the processes of
   their creation throughout the various layers of time embodied in their
   fabric. Despite the extensive use of digital tools within its workflows,
   building archeology has not yet embraced the digital age as firmly as
   other disciplines. While the research community has long been
   interconnected via societies and conferences, there still is no digital
   platform for the overarching valorisation of scientific building
   documentations. The project baureka.online, a research data repository,
   catalogue and archive for building archeology in the German-speaking
   area, seeks to provide an innovative answer to this desideratum.},
Publisher = {CASPUR-CIBER PUBL},
Address = {CASPUR-CIBER PUBL, ROMA, 00000, ITALY},
Type = {Article},
Language = {English},
Affiliation = {Naujokat, A (Corresponding Author), Rheinisch Westfalische TH Aachen, Aachen, Germany.
   Naujokat, Anke; Glitsch, Tobias; Martin, Felix, Rheinisch Westfalische TH Aachen, Aachen, Germany.
   Schlimme, Hermann, Tech Univ Berlin, Berlin, Germany.},
DOI = {10.2423/i22394303v10n1p43},
ISSN = {2239-4303},
Keywords = {building archaeology; research data repository; open access; metadata
   model; research community activation; research data indexing},
Research-Areas = {Arts \& Humanities - Other Topics},
Web-of-Science-Categories  = {Humanities, Multidisciplinary},
Affiliations = {RWTH Aachen University; Technical University of Berlin},
ORCID-Numbers = {Glitsch, Tobias/0000-0002-9911-2955
   Naujokat, Anke/0000-0003-1687-8419},
Number-of-Cited-References = {18},
Times-Cited = {2},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {6},
Journal-ISO = {SCIRES-IT},
Doc-Delivery-Number = {MY7TA},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000558617400006},
DA = {2024-01-15},
}

@article{ WOS:001084688400006,
Author = {Pinto, Fabiana de Melo Amaral Goncalves},
Title = {Publication of research data in nursing: new practices in open science},
Journal = {ENCONTROS BIBLI-REVISTA ELETRONICA DE BIBLIOTECONOMIA E CIENCIA DA
   INFORMACAO},
Year = {2023},
Volume = {28},
Abstract = {Objective: It presents data regarding the mapping of publication of
   research data by the Nursing area via datapaper, in scientific journals,
   and dataset, in a data repository.Method: Data were extracted from the
   interface of the following databases via the Capes Journal Portal: Web
   of science, Science direct, Scopus, Lilacs, Medline and Cinahl. The
   multidisciplinary repositories: Figshare, Dryade and Zenodo were also
   used as a source for data extraction.Result: Based on systematized
   searches directly in the interfaces of the cited sources, the document
   typologies pointed out in the article (datapapers and datasets) were
   structured in a .csv type file available in the Figshare repository
   under the DOI
   (https://doi.org/10.6084/m9.figshare.19790425.v3).Conclusions: The
   research data was organized based on the Dublin Core metadata standards,
   in addition to authorial metadata created to meet the research
   objective. In textual and numerical format, they consist of secondary
   data extracted from the interfaces of the cited sources on the field of
   Nursing.},
Publisher = {UNIV FEDERAL SANTA CATARINA},
Address = {CAMPUS UNIVERSITARIO REITOR JOAO DAVID FERREIRA LIMA, FLORIANOPOLIS, SC
   88010-970, BRAZIL},
Type = {Article},
Language = {Portuguese},
Affiliation = {Pinto, FDAG (Corresponding Author), Univ Fed Fluminense, Niteroi, RJ, Brazil.
   Pinto, Fabiana de Melo Amaral Goncalves, Univ Fed Fluminense, Niteroi, RJ, Brazil.},
DOI = {10.5007/1518-2924.2023.e93296},
Article-Number = {e93296},
EISSN = {1518-2924},
Keywords = {Publication of research data; Nursing; Search data; Data article;
   Research Data set},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {fabianamelo@id.uff.br},
Affiliations = {Universidade Federal Fluminense},
Number-of-Cited-References = {13},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Encontros Bibli},
Doc-Delivery-Number = {U4RM3},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001084688400006},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000654763200030,
Author = {Tomas Navarro-Carrion, Jose and Leon-Cadena, Paul and Ramon-Morte,
   Alfredo},
Title = {Open data repositories and Geo Small Data for mapping the wildfire risk
   exposure in wildland urban interface (WUI) in Spain: A case study in the
   Valencian Region},
Journal = {REMOTE SENSING APPLICATIONS-SOCIETY AND ENVIRONMENT},
Year = {2021},
Volume = {22},
Month = {APR},
Abstract = {The risk of forest fires in areas of wildland urban-interface (WUI.) is
   increasing due to the increase in urbanized areas and the progressive
   abandonment of traditional farming and forest uses. The global increase
   in catastrophic episodes in regions with a Mediterranean climate is
   worrying. Resilient towns and villages have given way to extensive and
   scattered residential estates that are in contact with forest fuel.
   These changes in the landscape when added to those of the climate,
   increase the danger of what some call `igneous storms'. The risk in many
   areas has increased greatly in the last few decades. It is necessary to
   limit the growing exposure to this type of risk - and geographical
   information resources are essential for determining the territorial
   magnitude of the problem. Official libraries offering remote sensing
   data or geographical databases on land use and land cover (LULC) may be
   the best option (although accessing this data is complex for many end
   users). This research proposes identifying areas exposed to fire risk in
   the wildland-urban interface (WUI) through the automated integration of
   massive data from official geographic information sources. The
   application of this study to the region of Valencia (Spain) shows that
   the integration of these official sources of geographical information
   can achieve the objective at a detailed scale with relatively short
   processing times and for large geographical areas (approximately 8 h
   required to process about 70 Gb of LIDAR data). Geo Small Data
   techniques for the process of large datasets and its application to the
   objective of the study have been the best way to automate the analysis
   of lidar point clouds, with more than 5 billion echoes, through the use
   of free and open tools, containerization technologies, parallel
   processing and specific python libraries for geospatial data management.
   The LIDAR data has provided the necessary geometric definition to
   complement and improve the WUI area map from the reclassification of
   hundreds of thousands of polygons from the official Spanish land use
   geodatabase (SIOSE), achieving a map scale of more than 1: 25,000, for
   its part, the quality of the SIOSE geodatabase has allowed us to reduce
   the total LIDAR data to process by 97.8\%.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Ramon-Morte, A (Corresponding Author), Ave Escandinavia 41,B-79, Alicante 03130, Spain.
   Tomas Navarro-Carrion, Jose; Ramon-Morte, Alfredo, Univ Alicante, Geog Interuniversitary Inst, Geomat Lab, Alicante, Spain.
   Leon-Cadena, Paul, Univ Armed Forces ESPE, Minist Environm \& Water, Forestry Directorate, Quito, Ecuador.},
DOI = {10.1016/j.rsase.2021.100500},
EarlyAccessDate = {APR 2021},
Article-Number = {100500},
ISSN = {2352-9385},
Keywords = {Natural risks; LIDAR; SIOSE; Land use and land cover; Geodatabases},
Keywords-Plus = {EUROPE IMPLICATIONS; LIDAR; FIRES; PREVENTION; LANDSCAPE; PATTERNS;
   HAZARD},
Research-Areas = {Environmental Sciences \& Ecology; Remote Sensing},
Web-of-Science-Categories  = {Environmental Sciences; Remote Sensing},
Author-Email = {alfredo.ramon@ua.es},
Affiliations = {Universitat d'Alacant},
Funding-Acknowledgement = {Spanish Ministry of Economy and Competitiveness (Project SIOSE-INNOVA
   AEI/FEDER.UE) {[}CSO 2016-79420-R]},
Funding-Text = {This work was supported by grants from the Spanish Ministry of Economy
   and Competitiveness (Project SIOSE-INNOVA - CSO 201679420-R
   AEI/FEDER.UE) and the methodology has been developed by the project
   research team. The cartographic result has been collected in an
   unpublished work that has been awarded the XII Edition `Pare Tosca'
   Cartography Prize of the Valencian Government (Valencian Cartographic
   Institute - ICV).},
Number-of-Cited-References = {72},
Times-Cited = {6},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Remote Sens. Appl.-Soc. Environ.},
Doc-Delivery-Number = {SI3YL},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000654763200030},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000889055200001,
Author = {Harrieder, Eva-Maria and Kretschmer, Fleming and Dunn, Warwick and
   Boecker, Sebastian and Witting, Michael},
Title = {Critical assessment of chromatographic metadata in publicly available
   metabolomics data repositories},
Journal = {METABOLOMICS},
Year = {2022},
Volume = {18},
Number = {12},
Month = {NOV 27},
Abstract = {Introduction The structural identification of metabolites represents one
   of the current bottlenecks in non-targeted liquid chromatography-mass
   spectrometry (LC-MS) based metabolomics. The Metabolomics Standard
   Initiative has developed a multilevel system to report confidence in
   metabolite identification, which involves the use of MS, MS/MS and
   orthogonal data. Limitations due to similar or same fragmentation
   pattern (e.g. isomeric compounds) can be overcome by the additional
   orthogonal information of the retention time (RT), since it is a system
   property that is different for each chromatographic setup. Objectives In
   contrast to MS data, sharing of RT data is not as widespread. The
   quality of data and its (re-)useability depend very much on the quality
   of the metadata. We aimed to evaluate the coverage and quality of this
   metadata from public metabolomics repositories. Methods We acquired an
   overview on the current reporting of chromatographic separation
   conditions. For this purpose, we defined the following information as
   important details that have to be provided: column name and dimension,
   flow rate, temperature, composition of eluents and gradient. Results We
   found that 70\% of descriptions of the chromatographic setups are
   incomplete (according to our definition) and an additional 10\% of the
   descriptions contained ambiguous and/or incorrect information.
   Accordingly, only about 20\% of the descriptions allow further (re-)use
   of the data, e.g. for RT prediction. Therefore, we have started to
   develop a unified and standardized notation for chromatographic metadata
   with detailed and specific description of eluents, columns and
   gradients. Conclusion Reporting of chromatographic metadata is currently
   not unified. Our recommended suggestions for metadata reporting will
   enable more standardization and automatization in future reporting.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Witting, M (Corresponding Author), Helmholtz Zentrum Munchen, Metabol \& Prote Core, Ingolstadter Landstr 1, D-85764 Neuherberg, Germany.
   Witting, M (Corresponding Author), Tech Univ Munich, TUM Sch Life Sci, Chair Analyt Food Chem, Maximus Von Imhof Forum 2, D-85354 Freising Weihenstephan, Germany.
   Harrieder, Eva-Maria, Helmholtz Zentrum Munchen, Res Unit Analyt BioGeoChem, Ingolstadter Landstr 1, D-85764 Neuherberg, Germany.
   Kretschmer, Fleming; Boecker, Sebastian, Friedrich Schiller Univ Jena, Chair Bioinformat, Ernst Abbe Pl 2, D-07743 Jena, Germany.
   Dunn, Warwick, Univ Liverpool, Inst Syst Mol \& Integrat Biol, Dept Biochem \& Syst Biol, Liverpool L69 7ZB, Merseyside, England.
   Witting, Michael, Helmholtz Zentrum Munchen, Metabol \& Prote Core, Ingolstadter Landstr 1, D-85764 Neuherberg, Germany.
   Witting, Michael, Tech Univ Munich, TUM Sch Life Sci, Chair Analyt Food Chem, Maximus Von Imhof Forum 2, D-85354 Freising Weihenstephan, Germany.},
DOI = {10.1007/s11306-022-01956-x},
Article-Number = {97},
ISSN = {1573-3882},
EISSN = {1573-3890},
Keywords = {Data reuse; Retention time; Repositories; Metabolomics; LC-MS},
Keywords-Plus = {MASS; STANDARDS},
Research-Areas = {Endocrinology \& Metabolism},
Web-of-Science-Categories  = {Endocrinology \& Metabolism},
Author-Email = {michael.witting@helmholtz-muenchen.de},
Affiliations = {Helmholtz Association; Helmholtz-Center Munich - German Research Center
   for Environmental Health; Friedrich Schiller University of Jena;
   University of Liverpool; Helmholtz Association; Helmholtz-Center Munich
   - German Research Center for Environmental Health; Technical University
   of Munich},
ORCID-Numbers = {Kretschmer, Fleming/0000-0001-8523-6546
   Witting, Michael/0000-0002-1462-4426},
Funding-Acknowledgement = {DFG {[}WI 4382/10-1, BO 1910/23-1]; Projekt DEAL},
Funding-Text = {Open Access funding enabled and organized by Projekt DEAL. The project
   was supported by DFG Grant BO 1910/23-1 to Sebastian Bocker and DFG
   Grant WI 4382/10-1 to Michael Witting.},
Number-of-Cited-References = {21},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Metabolomics},
Doc-Delivery-Number = {6M7PU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000889055200001},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000730820900007,
Author = {Kaur, Paramjeet and Nand, Parma and Naseer, Salman and Gardezi, Akber
   Abid and Alassery, Fawaz and Hamam, Habib and Cheikhrouhou, Omar and
   Shafiq, Muhammad},
Title = {Ontology-Based Semantic Search Framework for Disparate Datasets},
Journal = {INTELLIGENT AUTOMATION AND SOFT COMPUTING},
Year = {2022},
Volume = {32},
Number = {3},
Pages = {1717-1728},
Abstract = {The public sector provides open data to create new opportunities,
   sti-mulate innovation, and implement new solutions that benefit academia
   and society. However, open data is usually available in large quantities
   and often lacks quality, accuracy, and completeness. It may be difficult
   to find the right data to analyze a target. There are many rich open
   data repositories, but they are difficult to understand and use because
   these data can only be used with a complex set of keyword search
   options, and even then, irrelevant or insufficient data may even-tually
   be retrieved. To alleviate this situation, ontology-based semantic
   search has been proven to be an effective way to improve the quality of
   related content queries in such repositories. In this paper, we propose
   a new method of semantic linking and storing open government datasets of
   New Zealand's agriculture, land and rainfall sectors based on the use of
   ontology. The generated ontology can con-struct integrated data, in
   which a unified query can be applied to extract richer and more useful
   information. To validate our model, we showed how to link ontology
   manually and automatically. Manual linking requires domain experts, and
   auto-matic linking reduces the overhead of relying on domain experts to
   manually link concepts. The results of this method are promising in
   terms of improving data quality and search efficiency. In future, the
   proposed model can be integrated with other domain ontologies.},
Publisher = {TECH SCIENCE PRESS},
Address = {871 CORONADO CENTER DR, SUTE 200, HENDERSON, NV 89052 USA},
Type = {Article},
Language = {English},
Affiliation = {Shafiq, M (Corresponding Author), Yeungnam Univ, Dept Informat \& Commun Engn, Gyongsan 38541, South Korea.
   Kaur, Paramjeet; Nand, Parma, Auckland Univ Technol, Auckland 1010, New Zealand.
   Naseer, Salman, Univ Punjab, Dept Informat Technol, Gujranwala Campus, Gujranwala 52250, Pakistan.
   Gardezi, Akber Abid, COMSATS Univ Islamabad, Dept Comp Sci, Islamabad 45550, Pakistan.
   Alassery, Fawaz, Taif Univ, Coll Comp \& Informat Technol, Dept Comp Engn, At Taif, Saudi Arabia.
   Hamam, Habib, Moncton Univ, Fac Engn, Moncton, NB E1A 3E9, Canada.
   Cheikhrouhou, Omar, Univ Sfax, Natl Sch Engineers Sfax, CES Lab, Sfax 3038, Tunisia.
   Shafiq, Muhammad, Yeungnam Univ, Dept Informat \& Commun Engn, Gyongsan 38541, South Korea.},
DOI = {10.32604/iasc.2022.023063},
ISSN = {1079-8587},
EISSN = {2326-005X},
Keywords = {Open data; ontology; linked open data; semantic search},
Keywords-Plus = {WEB},
Research-Areas = {Automation \& Control Systems; Computer Science},
Web-of-Science-Categories  = {Automation \& Control Systems; Computer Science, Artificial Intelligence},
Author-Email = {shafiq@ynu.ac.kr},
Affiliations = {Auckland University of Technology; COMSATS University Islamabad (CUI);
   Taif University; Universite de Sfax; Ecole Nationale dIngenieurs de Sfax
   (ENIS); Yeungnam University},
ResearcherID-Numbers = {Naseer, Salman/AAI-1203-2020
   Hamam, Habib/C-1761-2019},
ORCID-Numbers = {Naseer, Salman/0000-0003-2153-8902
   Hamam, Habib/0000-0002-5320-1012},
Funding-Acknowledgement = {Taif University (in Taif, Saudi Arabia) {[}TURSP-2020/150]},
Funding-Text = {This work was supported by Taif University (in Taif, Saudi Arabia)
   through the Researchers Supporting Project Number (TURSP-2020/150) .},
Number-of-Cited-References = {23},
Times-Cited = {3},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {12},
Journal-ISO = {Intell. Autom. Soft Comput.},
Doc-Delivery-Number = {XP4EW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000730820900007},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000625306900001,
Author = {Madeyski, Lech and Lewowski, Tomasz and Kitchenham, Barbara},
Title = {OECD Recommendation's draft concerning access to research data from
   public funding: A review},
Journal = {BULLETIN OF THE POLISH ACADEMY OF SCIENCES-TECHNICAL SCIENCES},
Year = {2021},
Volume = {69},
Number = {1},
Month = {FEB},
Abstract = {Sharing research data from public funding is an important topic,
   especially now, during times of global emergencies like the COVID-19
   pandemic, when we need policies that enable rapid sharing of research
   data. Our aim is to discuss and review the revised Draft of the OECD
   Recommendation Concerning Access to Research Data from Public Funding.
   The Recommendation is based on ethical scientific practice, but in order
   to be able to apply it in real settings, we suggest several enhancements
   to make it more actionable. in particular, constant maintenance of
   provided software stipulated by the Recommendation is virtually
   impossible even for commercial software. Other major concerns are
   insufficient clarity regarding how to finance data repositories in joint
   private-public investments, inconsistencies between data security and
   user-friendliness of access, little focus on the reproducibility of
   submitted data, risks related to the mining of large data sets, and
   sensitive (particularly personal) data protection. In addition, we
   identify several risks and threats that need to be considered when
   designing and developing data platforms to implement the Recommendation
   (e.g., not only the descriptions of the data formats but also the data
   collection methods should be available). Furthermore, the non-even level
   of readiness of some countries for the practical implementation of the
   proposed Recommendation poses a risk of its delayed or incomplete
   implementation.},
Publisher = {POLSKA AKAD NAUK, POLISH ACAD SCI, DIV IV TECHNICAL SCIENCES PAS},
Address = {PL DEFILAD 1, WARSZAWA, 00-901, POLAND},
Type = {Review},
Language = {English},
Affiliation = {Madeyski, L (Corresponding Author), Wrocla Univ Sci \& Technol, Fac Comp Sci \& Management, Ul Wybrzeze Wyspianskiego 27, PL-50370 Wroclaw, Poland.
   Madeyski, Lech; Lewowski, Tomasz, Wrocla Univ Sci \& Technol, Fac Comp Sci \& Management, Ul Wybrzeze Wyspianskiego 27, PL-50370 Wroclaw, Poland.
   Kitchenham, Barbara, Keele Univ, Sch Comp \& Math, Keele ST5 5BG, Staffs, England.},
DOI = {10.24425/bpasts.2020.135401},
Article-Number = {e135401},
ISSN = {0239-7528},
EISSN = {2300-1917},
Keywords = {open data; open access; empirical research; data-driven research; data
   science},
Keywords-Plus = {DATA FABRICATION},
Research-Areas = {Engineering},
Web-of-Science-Categories  = {Engineering, Multidisciplinary},
Author-Email = {lech.madeyski@pwr.edu.pl},
Affiliations = {Keele University},
ResearcherID-Numbers = {Madeyski, Lech/D-4986-2012
   },
ORCID-Numbers = {Madeyski, Lech/0000-0003-3907-3357
   Lewowski, Tomasz/0000-0003-4897-1263},
Funding-Acknowledgement = {Presidium of the Committee on Informatics of the Polish Academy of
   Sciences},
Funding-Text = {The authors thank the reviewers for their helpful comments. The authors
   were invited to prepare their joint review presented in this work by the
   Presidium of the Committee on Informatics of the Polish Academy of
   Sciences.},
Number-of-Cited-References = {21},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Bull. Pol. Acad. Sci.-Tech. Sci.},
Doc-Delivery-Number = {QR6DM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000625306900001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000388798400001,
Author = {Busch, Julia A. and Bardaji, Raul and Ceccaroni, Luigi and Friedrichs,
   Anna and Piera, Jaume and Simon, Carine and Thijsse, Peter and Wernand,
   Marcel and van der Woerd, Hendrik J. and Zielinski, Oliver},
Title = {Citizen Bio-Optical Observations from Coast- and Ocean and Their
   Compatibility with Ocean Colour Satellite Measurements},
Journal = {REMOTE SENSING},
Year = {2016},
Volume = {8},
Number = {11},
Month = {NOV},
Abstract = {Marine processes are observed with sensors from both the ground and
   space over large spatio-temporal scales. Citizen-based contributions can
   fill observational gaps and increase environmental stewardship amongst
   the public. For this purpose, tools and methods for citizen science need
   to (1) complement existing datasets; and (2) be affordable, while
   appealing to different user and developer groups. In this article, tools
   and methods developed in the 7th Framework Programme of European Union
   (EU FP 7) funded project Citclops (citizens' observatories for coast and
   ocean optical monitoring) are reviewed. Tools range from a stand-alone
   smartphone app to devices with Arduino and 3-D printing, and hence are
   attractive to a diversity of users; from the general public to more
   specified maker-and open labware movements. Standardization to common
   water quality parameters and methods allows long-term storage in regular
   marine data repositories, such as SeaDataNet and EMODnet, thereby
   providing open data access. Due to the given intercomparability to
   existing remote sensing datasets, these tools are ready to complement
   the marine datapool. In the future, such combined satellite and citizen
   observations may set measurements by the engaged public in a larger
   context and hence increase their individual meaning. In a wider sense, a
   synoptic use can support research, management authorities, and societies
   at large.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Busch, JA (Corresponding Author), Carl von Ossietzky Univ Oldenburg, Inst Chem \& Biol Marine Environm, Schleusenstr 1, D-26382 Wilhelmshaven, Germany.
   Busch, JA (Corresponding Author), Jacobs Univ, Life Sci \& Chem, Campus Ring 1, D-28759 Bremen, Germany.
   Busch, Julia A.; Friedrichs, Anna; Zielinski, Oliver, Carl von Ossietzky Univ Oldenburg, Inst Chem \& Biol Marine Environm, Schleusenstr 1, D-26382 Wilhelmshaven, Germany.
   Busch, Julia A., Jacobs Univ, Life Sci \& Chem, Campus Ring 1, D-28759 Bremen, Germany.
   Bardaji, Raul; Piera, Jaume; Simon, Carine, Spanish Natl Res Council ICM CSIC, Inst Marine Sci, Barcelona 08003, Spain.
   Ceccaroni, Luigi, 1000001 Labs, Alzina 52, Barcelona 08024, Spain.
   Thijsse, Peter, MARIS, Kon Julianalaan 345A, NL-2273 JJ Voorburg, Netherlands.
   Wernand, Marcel, Royal Netherlands Inst Sea Res NIOZ, POB 59, NL-1790 AB Den Burg, Netherlands.
   van der Woerd, Hendrik J., Vrije Univ Amsterdam, Inst Environm Studies IVM, De Boelelaan 1087, NL-1081 HV Amsterdam, Netherlands.},
DOI = {10.3390/rs8110879},
Article-Number = {879},
EISSN = {2072-4292},
Keywords = {citizen's applications for earth surveillance; smartphones; open
   labware; interoperability; aquatic optics; incentives to mobilize the
   crowd; emerging technologies; data repositories; DIY; open access},
Keywords-Plus = {DIFFUSE ATTENUATION COEFFICIENT; NATURAL-WATERS; CLASSIFICATION;
   SEAWIFS; MERIS; MODIS},
Research-Areas = {Environmental Sciences \& Ecology; Geology; Remote Sensing; Imaging
   Science \& Photographic Technology},
Web-of-Science-Categories  = {Environmental Sciences; Geosciences, Multidisciplinary; Remote Sensing;
   Imaging Science \& Photographic Technology},
Author-Email = {Julia.Busch@uni-oldenburg.de
   bardaji@icm.csic.es
   luigi@10000011abs.org
   anna.friedrichs@uni-oldenburg.de
   jpiera@icm.csic.es
   carine.simon@csic.es
   peter@maris.nl
   marcel.wernand@nioz.n1
   h.j.vander.woerd@vu.nl
   oliver.zielinski@uni-oldenburg.de},
Affiliations = {Carl von Ossietzky Universitat Oldenburg; Jacobs University; Consejo
   Superior de Investigaciones Cientificas (CSIC); CSIC - Centro
   Mediterraneo de Investigaciones Marinas y Ambientales (CMIMA); CSIC -
   Instituto de Ciencias del Mar (ICM); Utrecht University; Royal
   Netherlands Institute for Sea Research (NIOZ); Vrije Universiteit
   Amsterdam},
ResearcherID-Numbers = {Zielinski, Oliver/Q-2502-2018
   van der Woerd, Hans J/K-9812-2013
   Simon, Carine/L-1219-2014
   Piera, Jaume/I-1152-2015
   Piera, Jaume/AAP-4663-2021
   Zielinski, Oliver/P-4643-2019
   },
ORCID-Numbers = {Zielinski, Oliver/0000-0002-6018-5030
   van der Woerd, Hans J/0000-0002-8901-7567
   Simon, Carine/0000-0001-9951-5132
   Piera, Jaume/0000-0001-5818-9836
   Piera, Jaume/0000-0001-5818-9836
   Zielinski, Oliver/0000-0002-6018-5030
   Bardaji, Raul/0000-0002-0803-3427
   Wernand, Marcel R./0000-0002-1331-9569
   Ceccaroni, Luigi/0000-0002-3116-0811},
Funding-Acknowledgement = {EC-FP7 Programme {[}308469]},
Funding-Text = {The Citclops project received funding by the EC-FP7 Programme, grant
   agreement No. 308469. In particular, the authors thank all citizens and
   project supporters for their valuable suggestions on modifications of
   the tools during workshops and training events.},
Number-of-Cited-References = {40},
Times-Cited = {39},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {33},
Journal-ISO = {Remote Sens.},
Doc-Delivery-Number = {ED4DS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000388798400001},
OA = {Green Published, gold, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000426038000001,
Author = {Martone, Maryann E. and Garcia-Castro, Alexander and VandenBos, Gary R.},
Title = {Data Sharing in Psychology},
Journal = {AMERICAN PSYCHOLOGIST},
Year = {2018},
Volume = {73},
Number = {2},
Pages = {111-125},
Month = {FEB-MAR},
Abstract = {Routine data sharing, defined here as the publication of the primary
   data and any supporting materials required to interpret the data
   acquired as part of a research study, is still in its infancy in
   psychology, as in many domains. Nevertheless, with increased scrutiny on
   reproducibility and more funder mandates requiring sharing of data, the
   issues surrounding data sharing are moving beyond whether data sharing
   is a benefit or a bane to science, to what data should be shared and
   how. Here, we present an overview of these issues, specifically focusing
   on the sharing of so-called ``long tail{''} data, that is, data
   generated by individual laboratories as part of largely
   hypothesis-driven research. We draw on experiences in other domains to
   discuss attitudes toward data sharing, cost-benefits, best practices and
   infrastructure. We argue that the publishing of data sets is an integral
   component of 21st-century scholarship. Moreover, although not all issues
   around how and what to share have been resolved, a consensus on
   principles and best practices for effective data sharing and the
   infrastructure for sharing many types of data are largely in place.},
Publisher = {AMER PSYCHOLOGICAL ASSOC},
Address = {750 FIRST ST NE, WASHINGTON, DC 20002-4242 USA},
Type = {Article},
Language = {English},
Affiliation = {Martone, ME (Corresponding Author), Univ Calif San Diego, Dept Neurosci, San Diego, CA 92093 USA.
   Martone, Maryann E., Univ Calif San Diego, Dept Neurosci, San Diego, CA 92093 USA.
   Garcia-Castro, Alexander, Univ Politecn Madrid, Ontol Engn Grp, Madrid, Spain.
   VandenBos, Gary R., Amer Psychol Assoc, Washington, DC 20036 USA.},
DOI = {10.1037/amp0000242},
ISSN = {0003-066X},
EISSN = {1935-990X},
Keywords = {open data; database; data repository; FAIR},
Keywords-Plus = {DATA CITATION; METAANALYSIS; REPLICATION; DEPRESSION},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Multidisciplinary},
Author-Email = {mmartone@ucsd.edu},
Affiliations = {University of California System; University of California San Diego;
   Universidad Politecnica de Madrid},
ORCID-Numbers = {Martone, Maryann/0000-0002-8406-3871},
Funding-Acknowledgement = {KOPAR, H-MSCA-IF {[}655009]},
Funding-Text = {Maryann E. Martone is a founder of SciCrunch.com, a technology company
   that provides services around the Research Resource Identifiers (RRIDs)
   referenced in Figure 1. Alexander Garcia-Castro acknowledges the KOPAR,
   H2020-MSCA-IF-2014, Grant Agreement 655009. We thank Jessica Nielson and
   Adam Ferguson for their helpful comments.},
Number-of-Cited-References = {66},
Times-Cited = {46},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {43},
Journal-ISO = {Am. Psychol.},
Doc-Delivery-Number = {FX4IT},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000426038000001},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000424713300015,
Author = {Spicer, Rachel A. and Steinbeck, Christoph},
Title = {A lost opportunity for science: journals promote data sharing in
   metabolomics but do not enforce it},
Journal = {METABOLOMICS},
Year = {2018},
Volume = {14},
Number = {1},
Month = {JAN},
Abstract = {Introduction Data sharing is being increasingly required by journals and
   has been heralded as a solution to the `replication crisis'.
   Objectives (i) Review data sharing policies of journals publishing the
   most metabolomics papers associated with open data and (ii) compare
   these journals' policies to those that publish the most metabolomics
   papers.
   Methods A PubMed search was used to identify metabolomics papers.
   Metabolomics data repositories were manually searched for linked
   publications.
   Results Journals that support data sharing are not necessarily those
   with the most papers associated to open metabolomics data.
   Conclusion Further efforts are required to improve data sharing in
   metabolomics.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Steinbeck, C (Corresponding Author), European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Steinbeck, C (Corresponding Author), Friedrich Schiller Univ, Inst Inorgan \& Analyt Chem, Jena, Germany.
   Spicer, Rachel A.; Steinbeck, Christoph, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Steinbeck, Christoph, Friedrich Schiller Univ, Inst Inorgan \& Analyt Chem, Jena, Germany.},
DOI = {10.1007/s11306-017-1309-5},
Article-Number = {16},
ISSN = {1573-3882},
EISSN = {1573-3890},
Keywords = {Data sharing; Open data; Metabolomics; Journal},
Keywords-Plus = {REPOSITORY; STANDARDS; REUSE},
Research-Areas = {Endocrinology \& Metabolism},
Web-of-Science-Categories  = {Endocrinology \& Metabolism},
Author-Email = {christoph.steinbeck@uni-jena.de},
Affiliations = {Wellcome Trust Sanger Institute; European Molecular Biology Laboratory
   (EMBL); Friedrich Schiller University of Jena},
ResearcherID-Numbers = {Steinbeck, Christoph/B-4131-2008
   },
ORCID-Numbers = {Spicer, Rachel/0000-0002-2807-8796
   Steinbeck, Christoph/0000-0001-6966-0814},
Number-of-Cited-References = {21},
Times-Cited = {13},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {19},
Journal-ISO = {Metabolomics},
Doc-Delivery-Number = {FV6SZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000424713300015},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000577157000003,
Author = {Perez-Riverol, Yasset and European Bioinformatics Community},
Title = {Toward a Sample Metadata Standard in Public Proteomics Repositories},
Journal = {JOURNAL OF PROTEOME RESEARCH},
Year = {2020},
Volume = {19},
Number = {10},
Pages = {3906-3909},
Month = {OCT 2},
Abstract = {Metadata is essential in proteomics data repositories and is crucial to
   interpret and reanalyze the deposited data sets. For every proteomics
   data set, we should capture at least three levels of metadata: (i) data
   set description, (ii) the sample to data files related information, and
   (iii) standard data file formats (e.g., mzIdentML, mzML, or mzTab).
   While the data set description and standard data file formats are
   supported by all ProteomeXchange partners, the information regarding the
   sample to data files is mostly missing. Recently, members of the
   European Bioinformatics Community for Mass Spectrometry (EuBIC) have
   created an open-source project called Sample to Data file format for
   Proteomics (https://github.com/bigbio/proteomics-metadata-standard/) to
   enable the standardization of sample metadata of public proteomics data
   sets. Here, the project is presented to the proteomics community, and we
   call for contributors, including researchers, journals, and consortiums
   to provide feedback about the format. We believe this work will improve
   reproducibility and facilitate the development of new tools dedicated to
   proteomics data analysis.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Perez-Riverol, Y (Corresponding Author), European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Cambridge CB10 1SD, England.
   Perez-Riverol, Yasset, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Cambridge CB10 1SD, England.},
DOI = {10.1021/acs.jproteome.0c00376},
ISSN = {1535-3893},
EISSN = {1535-3907},
Keywords = {sample metadata; experimental design; proteomics; multiomics; data
   repositories; proteomeXchange; open data; reproducibility; data
   reanalysis; bioinformatics; standards},
Keywords-Plus = {EXPERIMENTAL-DESIGN},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods},
Author-Email = {yperez@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL)},
ResearcherID-Numbers = {Perez-Riverol, Yasset/H-2873-2019},
ORCID-Numbers = {Perez-Riverol, Yasset/0000-0001-6579-6941},
Funding-Acknowledgement = {Wellcome Trust {[}208391/Z/17/Z]; Wellcome Trust {[}208391/Z/17/Z]
   Funding Source: Wellcome Trust},
Funding-Text = {Y.P.R. is supported by the Wellcome Trust, Grant 208391/Z/17/Z. We would
   like to acknowledge everyone involved in the EuBIC-MS community. This
   paper presents the project to the proteomics community, and the EuBIC
   group has been the organization (community) that created the project,
   including all of the steps for doing it, the discussion of the project,
   the use cases, the platform to discuss issues and annotate projects,
   etc. This platform and idea are what we are presenting here in this
   Perspective manuscript. Members of the community reviewed the
   Perspective and provided feedback about how to approach the proteomics
   community.},
Number-of-Cited-References = {11},
Times-Cited = {14},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {J. Proteome Res.},
Doc-Delivery-Number = {NZ5PF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000577157000003},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000753200400001,
Author = {Restrepo, David S. and Perez, Luis E. and Lopez, Diego M. and
   Vargas-Canas, Rubiel and Osorio-Valencia, Juan Sebastian},
Title = {Multi-Dimensional Dataset of Open Data and Satellite Images for
   Characterization of Food Security and Nutrition},
Journal = {FRONTIERS IN NUTRITION},
Year = {2022},
Volume = {8},
Month = {JAN 27},
Abstract = {BackgroundNutrition is one of the main factors affecting the development
   and quality of life of a person. From a public health perspective, food
   security is an essential social determinant for promoting healthy
   nutrition. Food security embraces four dimensions: physical availability
   of food, economic and physical access to food, food utilization, and the
   sustainability of the dimensions above. Integrally addressing the four
   dimensions is vital. Surprisingly most of the works focused on a single
   dimension of food security: the physical availability of food.
   ObjectiveThe paper proposes a multi-dimensional dataset of open data and
   satellite images to characterize food security in the department of
   Cauca, Colombia. MethodsThe food security dataset integrates multiple
   open data sources; therefore, the Cross-Industry Standard Process for
   Data Mining methodology was used to guide the construction of the
   dataset. It includes sources such as population and agricultural census,
   nutrition surveys, and satellite images. ResultsAn open multidimensional
   dataset for the Department of Cauca with 926 attributes and 9 rows (each
   row representing a Municipality) from multiple sources in Colombia, is
   configured. Then, machine learning models were used to characterize food
   security and nutrition in the Cauca Department. As a result, The Food
   security index calculated for Cauca using a linear regression model
   (Mean Absolute Error of 0.391) is 57.444 in a range between 0 and 100,
   with 100 the best score. Also, an approach for extracting four features
   (Agriculture, Habitation, Road, Water) of satellite images were tested
   with the ResNet50 model trained from scratch, having the best
   performance with a macro-accuracy, macro-precision, macro-recall, and
   macro-F1-score of 91.7, 86.2, 66.91, and 74.92\%, respectively.
   ConclusionIt shows how the CRISP-DM methodology can be used to create an
   open public health data repository. Furthermore, this methodology could
   be generalized to other types of problems requiring the creation of a
   dataset. In addition, the use of satellite images presents an
   alternative for places where data collection is challenging. The model
   and methodology proposed based on open data become a low-cost and
   effective solution that could be used by decision-makers, especially in
   developing countries, to support food security planning.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Restrepo, DS (Corresponding Author), Univ Cauca, Telemat Dept, Telemat Engn Res Grp, Popayan, Colombia.
   Restrepo, David S.; Perez, Luis E.; Lopez, Diego M., Univ Cauca, Telemat Dept, Telemat Engn Res Grp, Popayan, Colombia.
   Vargas-Canas, Rubiel, Univ Cauca, Instrumentat \& Control Res Grp, Dept Phys, Dynam Syst, Popayan, Colombia.
   Osorio-Valencia, Juan Sebastian, Univ Washington, Dept Global Hlth, Seattle, WA USA.},
DOI = {10.3389/fnut.2021.796082},
Article-Number = {796082},
ISSN = {2296-861X},
Keywords = {data mining; food security; machine learning; remote sensing; satellite
   imagery; dataset},
Keywords-Plus = {YIELD ESTIMATION},
Research-Areas = {Nutrition \& Dietetics},
Web-of-Science-Categories  = {Nutrition \& Dietetics},
Author-Email = {dsrestrepo@unicauca.edu.co},
Affiliations = {Universidad del Cauca; Universidad del Cauca; University of Washington;
   University of Washington Seattle},
ResearcherID-Numbers = {Lopez, Diego/GXV-9878-2022
   },
ORCID-Numbers = {Restrepo, David/0000-0002-3789-1957},
Number-of-Cited-References = {37},
Times-Cited = {5},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {14},
Journal-ISO = {Front. Nutr.},
Doc-Delivery-Number = {YW1SQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000753200400001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000809630100001,
Author = {Meyer, Tom and Garcia, Stephan Marticorena and Tzschaetzsch, Heiko and
   Herthum, Helge and Shahryari, Mehrgan and Stencel, Lisa and Braun,
   Juergen and Kalra, Prateek and Kolipaka, Arunark and Sack, Ingolf},
Title = {Comparison of inversion methods in MR elastography: An open-access
   pipeline for processing multifrequency shear-wave data and demonstration
   in a phantom, human kidneys, and brain},
Journal = {MAGNETIC RESONANCE IN MEDICINE},
Year = {2022},
Volume = {88},
Number = {4},
Pages = {1840-1850},
Month = {OCT},
Abstract = {Purpose Magnetic resonance elastography (MRE) maps the viscoelastic
   properties of soft tissues for diagnostic purposes. However, different
   MRE inversion methods yield different results, which hinder comparison
   of values, standardization, and establishment of quantitative MRE
   markers. Here, we introduce an expandable, open-access, webserver-based
   platform that offers multiple inversion techniques for multifrequency,
   3D MRE data. Methods The platform comprises a data repository and
   standard MRE inversion methods including local frequency estimation
   (LFE), direct-inversion based multifrequency dual elasto-visco (MDEV)
   inversion, and wavenumber-based (k-) MDEV. The use of the platform is
   demonstrated in phantom data and in vivo multifrequency MRE data of the
   kidneys and brains of healthy volunteers. Results Detailed maps of
   stiffness were generated by all inversion methods showing similar detail
   of anatomy. Specifically, the inner renal cortex had higher shear wave
   speed (SWS) than renal medulla and outer cortex without lateral
   differences. k-MDEV yielded higher SWS values than MDEV or LFE (full
   kidney/brain k-MDEV: 2.71 +/- 0.19/1.45 +/- 0.14 m/s, MDEV: 2.14 +/-
   0.16/0.99 +/- 0.11 m/s, LFE: 2.12 +/- 0.15/0.89 +/- 0.06 m/s).
   Conclusion The freely accessible platform supports the comparison of MRE
   results obtained with different inversion methods, filter thresholds, or
   excitation frequencies, promoting reproducibility in MRE across
   community-developed methods.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Sack, I (Corresponding Author), Charite Univ Med Berlin, Dept Radiol, Charitepl 1, D-10117 Berlin, Germany.
   Meyer, Tom; Garcia, Stephan Marticorena; Tzschaetzsch, Heiko; Shahryari, Mehrgan; Stencel, Lisa; Sack, Ingolf, Charite Univ Med Berlin, Dept Radiol, Charitepl 1, D-10117 Berlin, Germany.
   Herthum, Helge; Braun, Juergen, Charite Univ Med Berlin, Inst Med Informat, Berlin, Germany.
   Kalra, Prateek; Kolipaka, Arunark, Ohio State Univ, Dept Biomed Engn, Columbus, OH 43210 USA.
   Kalra, Prateek; Kolipaka, Arunark, Ohio State Univ, Dept Radiol, Wexner Med Ctr, Columbus, OH 43210 USA.},
DOI = {10.1002/mrm.29320},
EarlyAccessDate = {JUN 2022},
ISSN = {0740-3194},
EISSN = {1522-2594},
Keywords = {direct inversion; local frequency estimation; MRE; multifrequency
   magnetic resonance elastography; quantitative imaging biomarkers;
   viscoelasticity},
Keywords-Plus = {MAGNETIC-RESONANCE ELASTOGRAPHY; STIFFNESS},
Research-Areas = {Radiology, Nuclear Medicine \& Medical Imaging},
Web-of-Science-Categories  = {Radiology, Nuclear Medicine \& Medical Imaging},
Author-Email = {ingolf.sack@charite.de},
Affiliations = {Free University of Berlin; Humboldt University of Berlin; Charite
   Universitatsmedizin Berlin; Free University of Berlin; Humboldt
   University of Berlin; Charite Universitatsmedizin Berlin; University
   System of Ohio; Ohio State University; University System of Ohio; Ohio
   State University},
ResearcherID-Numbers = {Herthum, Helge/JGL-8198-2023
   Braun, Jochen/F-1370-2013
   },
ORCID-Numbers = {Braun, Jochen/0000-0002-8886-078X
   Herthum, Helge/0000-0001-6494-0833
   Meyer, Tom/0000-0002-2171-6791
   Tzschatzsch, Heiko/0000-0001-9458-2221
   Sack, Ingolf/0000-0003-2460-1444
   Braun, Jurgen/0000-0001-5183-7546},
Funding-Acknowledgement = {German Research Foundation {[}GRK2260, SFB1340]},
Funding-Text = {German Research Foundation, Grant/Award Number: GRK2260 BIOQIC, SFB1340},
Number-of-Cited-References = {42},
Times-Cited = {8},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Magn. Reson. Med.},
Doc-Delivery-Number = {3G4NC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000809630100001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000361776200005,
Author = {Michener, William K.},
Title = {Ecological data sharing},
Journal = {ECOLOGICAL INFORMATICS},
Year = {2015},
Volume = {29},
Number = {1},
Pages = {33-44},
Month = {SEP},
Abstract = {Data sharing is the practice of making data available for use by others.
   Ecologists are increasingly generating and sharing an immense volume of
   data. Such data may serve to augment existing data collections and can
   be used for synthesis efforts such as meta-analysis, for parameterizing
   models, and for verifying research results (Le., study reproducibility).
   Large volumes of ecological data may be readily available through
   institutions or data repositories that are the most comprehensive
   available and can serve as the core of ecological analysis. Ecological
   data are also employed outside the research context and are used for
   decision-making, natural resource management, education, and other
   purposes. Data sharing has a long history in many domains such as
   oceanography and the biodiversity sciences (e.g., taxonomic data and
   museum specimens), but has emerged relatively recently in the ecological
   sciences.
   A review of several of the large international and national ecological
   research programs that have emerged since the mid-1900s highlights the
   initial failures and more recent successes as well as the underlying
   causes from a near absence of effective policies to the emergence of
   community and data sharing policies coupled with the development and
   adoption of data and metadata standards and enabling tools.
   Sociocultural change and the move towards more open science have evolved
   more rapidly over the past two decades in response to new requirements
   set forth by governmental organizations, publishers and professional
   societies. As the scientific culture has changed so has the
   cyberinfrastructure landscape. The introduction of community-based data
   repositories, data and metadata standards, software tools, persistent
   identifiers, and federated search and discovery have all helped
   promulgate data sharing. Nevertheless, there are many challenges and
   opportunities especially as we move towards more open science.
   Cyberinfrastructure challenges include a paucity of easy-to-use metadata
   management systems, significant difficulties in assessing data quality
   and provenance, and an absence of analytical and visualization
   approaches that facilitate data integration and harmonization.
   Challenges and opportunities abound in the sociocultural arena where
   funders, researchers, and publishers all have a stake in clarifying
   policies, roles and responsibilities, as well as in incentivizing data
   sharing. A set of best practices and examples of software tools are
   presented that can enable research transparency, reproducibility and new
   knowledge by facilitating idea generation, research planning, data
   management and the dissemination of data and results. (C) 2015 The
   Author. Published by Elsevier B.V.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Michener, WK (Corresponding Author), Univ New Mexico, Coll Univ Lib \& Learning Sci, MSCO4 2815, Albuquerque, NM 87131 USA.
   Univ New Mexico, Coll Univ Lib \& Learning Sci, Albuquerque, NM 87131 USA.},
DOI = {10.1016/j.ecoinf.2015.06.010},
ISSN = {1574-9541},
EISSN = {1878-0512},
Keywords = {Data publication; Data sharing; Information technology; Metadata; Open
   access; Policy},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {william.michener@gmail.com},
Affiliations = {University of New Mexico},
Funding-Acknowledgement = {NSF {[}IIA-1301346, IIA-1329470, ACI-1430508]; Direct For Computer \&
   Info Scie \& Enginr; Office of Advanced Cyberinfrastructure (OAC)
   {[}1430508] Funding Source: National Science Foundation; Office Of The
   Director; Office of Integrative Activities {[}1301346] Funding Source:
   National Science Foundation},
Funding-Text = {This work was supported by the NSF IIA-1301346, IIA-1329470, and
   ACI-1430508. Special thanks to Professor Friedrich Recknagel for his
   encouragement and input, as well as B. Kimbell and two anonymous
   reviewers for their insightful suggestions.},
Number-of-Cited-References = {83},
Times-Cited = {126},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {86},
Journal-ISO = {Ecol. Inform.},
Doc-Delivery-Number = {CS0TX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000361776200005},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000904670800013,
Author = {Sainz-Pardo Diaz, Judith and Lopez Garcia, Alvaro},
Title = {Study of the performance and scalability of federated learning for
   medical imaging with intermittent clients},
Journal = {NEUROCOMPUTING},
Year = {2023},
Volume = {518},
Pages = {142-154},
Month = {JAN 21},
Abstract = {Federated learning is a data decentralization privacy-preserving
   technique used to perform machine or deep learning in a secure way. In
   this paper we present theoretical aspects about federated learning, such
   as the presentation of an aggregation operator, different types of
   federated learning, and issues to be taken into account in relation to
   the distribution of data from the clients, together with the exhaustive
   analysis of a use case where the number of clients varies. Specifically,
   a use case of medical image analysis is proposed, using chest X-ray
   images obtained from an open data repository. In addition to the
   advantages related to privacy, improvements in predictions (in terms of
   accuracy, loss and area under the curve) and reduction of execution
   times will be studied with respect to the classical case (the
   centralized approach). Different clients will be simulated from the
   training data, selected in an unbalanced manner. The results of
   considering three or ten clients are exposed and compared between them
   and against the centralized case. Two different problems related to
   intermittent clients are discussed, together with two approaches to be
   followed for each of them. Specifically, this type of problems may occur
   because in a real scenario some clients may leave the training, and
   others enter it, and on the other hand because of client technical or
   connectivity problems. Finally, improvements and future work in the
   field are proposed. (c) 2022 The Author(s). Published by Elsevier B.V.
   This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Díaz, JSP (Corresponding Author), CSIC UC, Inst Fis Cantabria IFCA, Avda Castros S-N, Santander 39005, Spain.
   Sainz-Pardo Diaz, Judith; Lopez Garcia, Alvaro, CSIC UC, Inst Fis Cantabria IFCA, Avda Castros S-N, Santander 39005, Spain.},
DOI = {10.1016/j.neucom.2022.11.011},
EarlyAccessDate = {NOV 2022},
ISSN = {0925-2312},
EISSN = {1872-8286},
Keywords = {Federated learning; Deep learning; Data decentralization; Data privacy},
Keywords-Plus = {PRIVACY},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Artificial Intelligence},
Affiliations = {Consejo Superior de Investigaciones Cientificas (CSIC); Universidad de
   Cantabria; CSIC - Instituto de Fisica de Cantabria (IFCA)},
ResearcherID-Numbers = {Sáinz-Pardo Díaz, Judith/JCE-0368-2023
   García, Álvaro López/G-4796-2016},
ORCID-Numbers = {Sáinz-Pardo Díaz, Judith/0000-0002-8387-578X
   García, Álvaro López/0000-0002-0013-4602},
Funding-Acknowledgement = {European Union {[}EU 2020/2094, 101058593]; Horizon Europe - Research
   Infrastructures (RIS) {[}101058593] Funding Source: Horizon Europe -
   Research Infrastructures (RIS)},
Funding-Text = {First, we would like to thank the reviewers for their comments, which
   have contributed to improve this work. The authors acknowledge the
   funding through the European Union-NextGen- erationEU (Regulation EU
   2020/2094) , through CSIC?s Global Health Platform (PTI + Salud Global)
   and the support from the pro- ject AI4EOSC ?Artificial Intelligence for
   the European Open Science Cloud? that has received funding from the
   European Union?s Hori- zon Europe research and innovation programme
   under grant agreement number 101058593.},
Number-of-Cited-References = {47},
Times-Cited = {6},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Neurocomputing},
Doc-Delivery-Number = {7J6DA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000904670800013},
OA = {Green Submitted, hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000316089200008,
Author = {Xia, Jingfeng and Liu, Ying},
Title = {Usage Patterns of Open Genomic Data},
Journal = {COLLEGE \& RESEARCH LIBRARIES},
Year = {2013},
Volume = {74},
Number = {2},
Pages = {195-206},
Month = {MAR},
Abstract = {This paper uses Genome Expression Omnibus (GEO), a data repository in
   biomedical sciences, to examine the usage patterns of open data
   repositories. It attempts to identify the degree of recognition of data
   reuse value and understand how e-science has impacted a large-scale
   scholarship. By analyzing a list of 1,211 publications that cite GEO
   data to support their independent studies, it discovers that free data
   can support a wealth of high-quality investigations, that the rate of
   open data use keeps growing over the years, and that scholars in
   different countries show different rates of complying with data-sharing
   policies.},
Publisher = {ASSOC COLL RESEARCH LIBRARIES},
Address = {50 E HURON ST, CHICAGO, IL 60611 USA},
Type = {Article},
Language = {English},
Affiliation = {Xia, JF (Corresponding Author), Indiana Univ, Sch Lib \& Informat Sci, Bloomington, IN 47405 USA.
   Xia, Jingfeng, Indiana Univ, Sch Lib \& Informat Sci, Bloomington, IN 47405 USA.
   Liu, Ying, Beijing Univ Posts \& Telecommun, Sch Econ \& Management, Beijing, Peoples R China.},
DOI = {10.5860/crl-324},
ISSN = {0010-0870},
EISSN = {2150-6701},
Keywords-Plus = {GENE-EXPRESSION; ACCESS; AVAILABILITY},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {xiaji@iupui.edu
   fantasysoar@gmail.com},
Affiliations = {Indiana University System; Indiana University Bloomington; Beijing
   University of Posts \& Telecommunications},
ORCID-Numbers = {Xia, Jingfeng/0000-0001-5605-4292},
Number-of-Cited-References = {47},
Times-Cited = {7},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {34},
Journal-ISO = {Coll. Res. Libr.},
Doc-Delivery-Number = {105RD},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000316089200008},
OA = {gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000691103000004,
Author = {Crystal-Ornelas, Robert and Varadharajan, Charuleka and Bond-Lamberty,
   Ben and Boye, Kristin and Burrus, Madison and Cholia, Shreyas and Crow,
   Michael and Damerow, Joan and Devarakonda, Ranjeet and Ely, Kim S. and
   Goldman, Amy and Heinz, Susan and Hendrix, Valerie and Kakalia, Zarine
   and Pennington, Stephanie C. and Robles, Emily and Rogers, Alistair and
   Simmonds, Maegen and Velliquette, Terri and Weierbach, Helen and
   Weisenhorn, Pamela and Welch, Jessica N. and Agarwal, Deborah A.},
Title = {A Guide to Using GitHub for Developing and Versioning Data Standards and
   Reporting Formats},
Journal = {EARTH AND SPACE SCIENCE},
Year = {2021},
Volume = {8},
Number = {8},
Month = {AUG},
Abstract = {Data standardization combined with descriptive metadata facilitate data
   reuse, which is the ultimate goal of the Findable, Accessible,
   Interoperable, and Reusable (FAIR) principles. Community data or
   metadata standards are increasingly created through an approach that
   emphasizes collaboration between various stakeholders. Such an approach
   requires platforms for collaboration on the development process that
   centers on sharing information and receiving feedback. Our objective in
   this study was to conduct a systematic review to identify data standards
   and reporting formats that use version control for developing data
   standards and to summarize common practices, particularly in earth and
   environmental sciences. Out of 108 data standards and reporting formats
   identified in our review, 32 used GitHub as the version control
   platform, and no other platforms were used. We found no universally
   accepted methodology for developing and publishing data standards. Many
   GitHub repositories did not use key features that could help developers
   to gather user feedback, or to create and revise standards that build on
   previous work. We provide guidance for community-driven standard
   development and associated documentation on GitHub based on a systematic
   review of existing practices.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Crystal-Ornelas, R (Corresponding Author), Lawrence Berkeley Natl Lab, Earth \& Environm Sci Area, Berkeley, CA 94720 USA.
   Crystal-Ornelas, Robert; Varadharajan, Charuleka; Burrus, Madison; Damerow, Joan; Kakalia, Zarine; Robles, Emily; Simmonds, Maegen; Weierbach, Helen, Lawrence Berkeley Natl Lab, Earth \& Environm Sci Area, Berkeley, CA 94720 USA.
   Bond-Lamberty, Ben; Pennington, Stephanie C., Univ Maryland, Pacific Northwest Natl Lab, Joint Global Change Res Inst, College Pk, MD 20742 USA.
   Boye, Kristin, SLAC Natl Accelerator Lab, Geochem \& Biogeochem Grp, Menlo Pk, CA USA.
   Cholia, Shreyas; Hendrix, Valerie; Agarwal, Deborah A., Lawrence Berkeley Natl Lab, Computat Res Div, Berkeley, CA USA.
   Crow, Michael; Devarakonda, Ranjeet; Heinz, Susan; Velliquette, Terri; Welch, Jessica N., Oak Ridge Natl Lab, Div Environm Sci, POB 2008, Oak Ridge, TN 37831 USA.
   Ely, Kim S.; Rogers, Alistair, Brookhaven Natl Lab, Environm \& Climate Sci Dept, Upton, NY 11973 USA.
   Goldman, Amy, Pacific Northwest Natl Lab, Richland, WA 99352 USA.
   Weisenhorn, Pamela, Argonne Natl Lab, Lemont, IL USA.},
DOI = {10.1029/2021EA001797},
Article-Number = {e2021EA001797},
EISSN = {2333-5084},
Keywords = {FAIR data; TRUST principles; open science; metadata; data repositories},
Research-Areas = {Astronomy \& Astrophysics; Geology},
Web-of-Science-Categories  = {Astronomy \& Astrophysics; Geosciences, Multidisciplinary},
Author-Email = {rcrystalornelas@lbl.gov},
Affiliations = {United States Department of Energy (DOE); Lawrence Berkeley National
   Laboratory; University System of Maryland; University of Maryland
   College Park; United States Department of Energy (DOE); Pacific
   Northwest National Laboratory; Stanford University; United States
   Department of Energy (DOE); SLAC National Accelerator Laboratory; United
   States Department of Energy (DOE); Lawrence Berkeley National
   Laboratory; United States Department of Energy (DOE); Oak Ridge National
   Laboratory; United States Department of Energy (DOE); Brookhaven
   National Laboratory; United States Department of Energy (DOE); Pacific
   Northwest National Laboratory; United States Department of Energy (DOE);
   Argonne National Laboratory},
ResearcherID-Numbers = {Varadharajan, Charuleka/G-3741-2015
   Ely, Kim S/C-7715-2019
   Rogers, Alistair/E-1177-2011
   Devarakonda, Ranjeet/E-5976-2016
   Crystal-Ornelas, Robert/AAK-3887-2020
   Crystal-Ornelas, Robert/HPH-4796-2023
   Pennington, Stephanie/AAX-1306-2020
   Ball-Damerow, Joan/X-7925-2018
   Bond-Lamberty, Benjamin/C-6058-2008
   Varadharajan, Charuleka/S-4238-2019
   Welch, Jessica/B-7356-2018
   },
ORCID-Numbers = {Varadharajan, Charuleka/0000-0002-4142-3224
   Ely, Kim S/0000-0002-3915-001X
   Rogers, Alistair/0000-0001-9262-7430
   Devarakonda, Ranjeet/0000-0003-2661-1937
   Crystal-Ornelas, Robert/0000-0002-6339-1139
   Crystal-Ornelas, Robert/0000-0002-6339-1139
   Pennington, Stephanie/0000-0003-2685-1092
   Ball-Damerow, Joan/0000-0003-2601-5043
   Bond-Lamberty, Benjamin/0000-0001-9525-4633
   Varadharajan, Charuleka/0000-0002-4142-3224
   Crow, Michael/0000-0002-7260-807X
   Boye, Kristin/0000-0003-2087-607X
   Simmonds, Maegen/0000-0001-7796-7154
   Robles, Emily/0000-0003-3720-6566
   Cholia, Shreyas/0000-0002-4775-8201
   Weierbach, Helen/0000-0001-6348-9120
   Welch, Jessica/0000-0002-5987-6387
   Velliquette, Terri/0000-0001-9855-5191},
Funding-Acknowledgement = {ESS-DIVE repository by the U.S. DOE's Office of Science Biological and
   Environmental Research {[}DE-AC02-05CH11231]; US Department of Energy
   {[}DE-SC0012704]; ESS-DIVE's Community Funds, through the Office of
   Biological and Environmental Research in the Department of Energy,
   Office of Science},
Funding-Text = {Robert Crystal-Ornelas, Charuleka Varadharajan, Shreyas Cholia, Valerie
   Hendrix, Joan Damerow, Madison Burrus, Zarine Kakalia, Emily Robles,
   Maegen Simmonds, and Deborah A. Agarwal were funded through the ESS-DIVE
   repository by the U.S. DOE's Office of Science Biological and
   Environmental Research under contract number DE-AC02-05CH11231. Kim S.
   Ely and Alistair Rogers were supported through the US Department of
   Energy contract number DE-SC0012704 to Brookhaven National Laboratory.
   Reporting format development was supported by ESS-DIVE's Community
   Funds, through the Office of Biological and Environmental Research in
   the Department of Energy, Office of Science. The authors thank Dr.
   Chelle Gentemann, Dr. Peter Desmet, and one anonymous reviewer for their
   insightful comments on our manuscript.},
Number-of-Cited-References = {45},
Times-Cited = {6},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {16},
Journal-ISO = {Earth Space Sci.},
Doc-Delivery-Number = {UJ2DP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000691103000004},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000945967800011,
Author = {d'Aquin, Mathieu and Kirstein, Fabian and Oliveira, Daniela and
   Schimmler, Sonja and Urbanek, Sebastian},
Title = {FAIREST: A Framework for Assessing Research Repositories},
Journal = {DATA INTELLIGENCE},
Year = {2023},
Volume = {5},
Number = {1},
Pages = {202-241},
Month = {MAR 8},
Abstract = {The open science movement has gained significant momentum within the
   last few years. This comes along with the need to store and share
   research artefacts, such as publications and research data. For this
   purpose, research repositories need to be established. A variety of
   solutions exist for implementing such repositories, covering diverse
   features, ranging from custom depositing workflows to social media-like
   functions. In this article, we introduce the FAIREST principles, a
   framework inspired by the well-known FAIR principles, but designed to
   provide a set of metrics for assessing and selecting solutions for
   creating digital repositories for research artefacts. The goal is to
   support decision makers in choosing such a solution when planning for a
   repository, especially at an institutional level. The metrics included
   are therefore based on two pillars: (1) an analysis of established
   features and functionalities, drawn from existing dedicated, general
   purpose and commonly used solutions, and (2) a literature review on
   general requirements for digital repositories for research artefacts and
   related systems. We further describe an assessment of 11 widespread
   solutions, with the goal to provide an overview of the current landscape
   of research data repository solutions, identifying gaps and research
   challenges to be addressed.},
Publisher = {MIT PRESS},
Address = {ONE ROGERS ST, CAMBRIDGE, MA 02142-1209 USA},
Type = {Article},
Language = {English},
Affiliation = {d'Aquin, M (Corresponding Author), Univ Lorraine, LORIA, CNRS, INRIA, F-54506 Nancy, France.
   d'Aquin, Mathieu, Univ Lorraine, LORIA, CNRS, INRIA, F-54506 Nancy, France.
   Kirstein, Fabian; Schimmler, Sonja; Urbanek, Sebastian, Fraunhofer FOKUS, D-10589 Berlin, Germany.
   Kirstein, Fabian; Schimmler, Sonja; Urbanek, Sebastian, Weizenbaum Inst Networked Soc, D-10623 Berlin, Germany.
   Oliveira, Daniela, Univ Lisbon, Fac Ciecias, LaSIGE, P-1749016 Lisbon, Portugal.},
DOI = {10.1162/dint\_a\_00159},
EISSN = {2641-435X},
Keywords = {research repositories; FAIR principles; open access; research data},
Keywords-Plus = {INSTITUTIONAL REPOSITORIES},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Author-Email = {mathieu.daquin@loria.fr},
Affiliations = {Universite de Lorraine; Inria; Centre National de la Recherche
   Scientifique (CNRS); Fraunhofer Gesellschaft; Fraunhofer Institute
   Center Schloss Birlinghoven; Universidade de Lisboa},
Funding-Acknowledgement = {Fundacao para a Ciencia e a Tecnologia through the LASIGE Research Unit
   {[}UIDB/00408/2020, UIDP/00408/2020]; Federal Ministry of Education and
   Research of Germany (BMBF) {[}16DII128]},
Funding-Text = {This research was supported by the Fundacao para a Ciencia e a
   Tecnologia through the LASIGE Research Unit, UIDB/00408/2020 and
   UIDP/00408/2020.This work was supported by the Federal Ministry of
   Education and Research of Germany (BMBF) under grant no. 16DII128
   ({''}Deutsches Internet-Institut{''}).},
Number-of-Cited-References = {35},
Times-Cited = {2},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Data Intell.},
Doc-Delivery-Number = {9R9KX},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000945967800011},
OA = {gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000805417800043,
Author = {Yucra, Daniel and Sotomayor, Julio and Mayhuasca, Jorge and Arroyo,
   Antonio and Chicasaca, Carmen and Marin, Wilson},
Title = {EVALUATION OF FREE TECHNOLOGIES FOR THE MANAGEMENT OF METADATA IN
   DIGITAL REPOSITORIES FOR GOVERNMENTAL ENTITIES},
Journal = {INTERNATIONAL JOURNAL OF EARLY CHILDHOOD SPECIAL EDUCATION},
Year = {2022},
Volume = {14},
Number = {3},
Pages = {5092-5098},
Abstract = {This article presents the results obtained from the evaluation of free
   technologies for the management of metadata in digital repositories for
   governmental entities. The methods and procedures consisted of a
   literature search on digital repository software for data and metadata
   management, testing and evaluation of alternative solutions, as well as
   considering functional requirements as a basis: cataloging and data and
   metadata management systems. The result of this work highlights the
   characteristics, capabilities, and functionalities of each software that
   presents resources for building a data repository, sharing data, and
   representing it to users. In addition, technical evaluation criteria for
   testing, evaluation, and selection are presented. This proposal allows
   government sector entities to achieve technological sovereignty and
   independence, in addition to promoting the publication of open data for
   open government management.},
Publisher = {ANADOLU UNIV},
Address = {INST FINE ARTS, ESKISEHIR, 26470, TURKEY},
Type = {Article},
Language = {English},
Affiliation = {Yucra, D (Corresponding Author), Sci Univ South, Lima, Peru.
   Yucra, Daniel, Sci Univ South, Lima, Peru.
   Sotomayor, Julio; Mayhuasca, Jorge, Natl Univ Federico Villarreal, San Miguel, Peru.
   Arroyo, Antonio, Natl Univ Altiplano, Puno, Peru.
   Chicasaca, Carmen, Alas Peruanas Univ, Pueblo Libre, Peru.
   Marin, Wilson, Cesar Vallejo Univ, Victor Larco Herrera Dis, Peru.},
DOI = {10.9756/INT-JECSE/V14I3.670},
ISSN = {1308-5581},
Keywords = {Digital Repository; Metadata; Open Data},
Research-Areas = {Education \& Educational Research},
Web-of-Science-Categories  = {Education, Special},
Author-Email = {dyucra@cientifica.edu.pe
   jsotomayor@unfv.edu.pe
   jmayhuasca@unfv.edu.pe
   arroyopaz@unap.edu.pe
   c\_chicasaca@alu.uap.edu.pe
   wmarinv@ucv.edu.pe},
Affiliations = {Universidad Cientifica del Sur (CIENTIFICA); Universidad Nacional del
   Altiplano; Universidad Alas Peruanas; Universidad Cesar Vallejo},
Number-of-Cited-References = {12},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Int. J. Early Child. Spec. Educ.},
Doc-Delivery-Number = {1U4XO},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000805417800043},
DA = {2024-01-15},
}

@article{ WOS:000796291800002,
Author = {Rapuano, Kristina M. and Conley, May I. and Juliano, Anthony C. and
   Conan, Gregory M. and Maza, Maria T. and Woodman, Kylie and Martinez,
   Steven A. and Earl, Eric and Perrone, Anders and Feczko, Eric and Fair,
   Damien A. and Watts, Richard and Casey, B. J. and Rosenberg, Monica D.},
Title = {An open-access accelerated adult equivalent of the ABCD Study
   neuroimaging dataset (a-ABCD)},
Journal = {NEUROIMAGE},
Year = {2022},
Volume = {255},
Month = {JUL 15},
Abstract = {As public access to longitudinal developmental datasets like the
   Adolescent Brain Cognitive Development StudySM (ABCD Study (R))
   increases, so too does the need for resources to benchmark
   time-dependent effects. Scan-to-scan changes observed with repeated
   imaging may reflect development but may also reflect practice effects,
   dayto-day variability in psychological states, and/or measurement noise.
   Resources that allow disentangling these time-dependent effects will be
   useful in quantifying actual developmental change. We present an
   accelerated adult equivalent of the ABCD Study dataset (a-ABCD) using an
   identical imaging protocol to acquire magnetic resonance imaging (MRI)
   structural, diffusion-weighted, resting-state and task-based data from
   eight adults scanned five times over five weeks. We report on the
   task-based imaging data ( n = 7). In-scanner stop-signal (SST), monetary
   incentive delay (MID), and emotional n-back (EN-back) task behavioral
   performance did not change across sessions. Post-scan recognition memory
   for emotional n-back stimuli, however, did improve as participants
   became more familiar with the stimuli. Functional MRI analyses revealed
   that patterns of task-based activation reflecting inhibitory control in
   the SST, reward success in the MID task, and working memory in the
   EN-back task were more similar within individuals across repeated scan
   sessions than between individuals. Within-subject, activity was more
   consistent across sessions during the EN-back task than in the SST and
   MID task, demonstrating differences in fMRI data reliability as a
   function of task. The a-ABCD dataset provides a unique testbed for
   characterizing the reliability of brain function, structure, and
   behavior across imaging modalities in adulthood and benchmarking
   neurodevelopmental change observed in the open-access ABCD Study.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Rapuano, KM; Rosenberg, MD (Corresponding Author), Yale Univ, Dept Psychol, New Haven, CT 06520 USA.
   Rosenberg, MD (Corresponding Author), Univ Chicago, Dept Psychol, Chicago, IL USA.
   Rapuano, Kristina M.; Conley, May I.; Maza, Maria T.; Woodman, Kylie; Martinez, Steven A.; Watts, Richard; Casey, B. J.; Rosenberg, Monica D., Yale Univ, Dept Psychol, New Haven, CT 06520 USA.
   Juliano, Anthony C., Univ Vermont, Dept Psychiat, Burlington, VT USA.
   Maza, Maria T., Univ N Carolina, Dept Psychol, Chapel Hill, NC USA.
   Woodman, Kylie, Univ Calif Santa Barbara, Dept Commun, Santa Barbara, CA USA.
   Martinez, Steven A., Temple Univ, Dept Psychol, Philadelphia, PA USA.
   Earl, Eric; Perrone, Anders, Oregon Hlth \& Sci Univ, Dept Psychiat, Portland, OR USA.
   Conan, Gregory M.; Perrone, Anders; Feczko, Eric; Fair, Damien A., Univ Minnesota Med Sch, Mason Inst Developing Brain, Minneapolis, MN USA.
   Feczko, Eric, Univ Minnesota Med Sch, Dept Pediat, Minneapolis, MN USA.
   Rosenberg, Monica D., Univ Chicago, Dept Psychol, Chicago, IL USA.},
DOI = {10.1016/j.neuroimage.2022.119215},
EarlyAccessDate = {APR 2022},
Article-Number = {119215},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords = {Development; Working memory; Inhibitory control; Reward processing; fMRI},
Keywords-Plus = {TEST-RETEST; FMRI; VARIABILITY; RELIABILITY},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {kristina.rapuano@yale.edu
   bj.casey@yale.edu
   mdrosenberg@uchicago.edu},
Affiliations = {Yale University; University of Vermont; University of North Carolina;
   University of North Carolina Chapel Hill; University of California
   System; University of California Santa Barbara; Pennsylvania
   Commonwealth System of Higher Education (PCSHE); Temple University;
   Oregon Health \& Science University; University of Minnesota System;
   University of Minnesota Twin Cities; University of Minnesota System;
   University of Minnesota Twin Cities; University of Chicago},
ResearcherID-Numbers = {Rosenberg, Monica D./J-6487-2019
   Earl, Eric/AAZ-3286-2021
   Watts, Richard/AEU-2679-2022
   },
ORCID-Numbers = {Rosenberg, Monica D./0000-0001-6179-4025
   Earl, Eric/0000-0001-5512-0083
   Conan, Gregory/0000-0002-3758-5562},
Funding-Acknowledgement = {National Institutes of Health {[}U01DA041022, U01DA041028, U01DA041048,
   U01DA041089, U01DA041106, U01DA041117, U01DA041120, U01DA041134,
   U01DA041148, U01DA041156, U01DA041174, U24DA041123, U24DA041147];
   National Institute of Mental Health of the National Institutes of Health
   from the National Institute of Drug Abuse {[}UG3-DA045251]; 
   {[}R25MH120869]},
Funding-Text = {Data used in the preparation of this article were obtained from the
   Adolescent Brain Cognitive Development (ABCD) Study (abcd-study.org) ,
   held in the NIMH Data Archive (NDA) . This is a multisite, longitudinal
   study designed to recruit more than 10,000 children ages 9-10 and follow
   them over 10 years into early adulthood. The ABCD Study is supported by
   the National Institutes of Health and additional federal partners under
   award numbers U01DA041022, U01DA041028, U01DA041048, U01DA041089,
   U01DA041106, U01DA041117, U01DA041120, U01DA041134, U01DA041148,
   U01DA041156, U01DA041174, U24DA041123, and U24DA041147. A full list of
   supporters is available at abcdstudy.org/nih-collaborators. A listing of
   participating sites and a complete listing of the study investigators
   can be found at abcdstudy.org/principal-investigators.html. ABCD
   consortium investigators designed and implemented the study and/or
   provided data but did not necessarily participate in analysis or writing
   of this report. This manuscript reflects the views of the authors and
   may not reflect the opinions or views of the NIH or ABCD consortium
   investigators. The ABCD data repository grows and changes over time. The
   ABCD data used in this report came from NIMH Data Archive Digital Object
   Identifier 10.15154/1504041. DOIs can be found at
   nda.nih.gov/study.html?id = 721. This research also benefited from the
   ABCD Workshop on Brain Development and Mental Health, supported by the
   National Institute of Mental Health of the National Institutes of Health
   under Award Number R25MH120869 and by UG3-DA045251 from the National
   Institute of Drug Abuse.},
Number-of-Cited-References = {53},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {1H1FN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000796291800002},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000359772700095,
Author = {Smedley, Damian and Haider, Syed and Durinck, Steffen and Pandini, Luca
   and Provero, Paolo and Allen, James and Arnaiz, Olivier and Awedh,
   Mohammad Hamza and Baldock, Richard and Barbiera, Giulia and Bardou,
   Philippe and Beck, Tim and Blake, Andrew and Bonierbale, Merideth and
   Brookes, Anthony J. and Bucci, Gabriele and Buetti, Iwan and Burge,
   Sarah and Cabau, Cedric and Carlson, Joseph W. and Chelala, Claude and
   Chrysostomou, Charalambos and Cittaro, Davide and Collin, Olivier and
   Cordova, Raul and Cutts, Rosalind J. and Dassi, Erik and Di Genova, Alex
   and Djari, Anis and Esposito, Anthony and Estrella, Heather and Eyras,
   Eduardo and Fernandez-Banet, Julio and Forbes, Simon and Free, Robert C.
   and Fujisawa, Takatomo and Gadaleta, Emanuela and Garcia-Manteiga, Jose
   M. and Goodstein, David and Gray, Kristian and Guerra-Assuncao, JoseE
   Afonso and Haggarty, Bernard and Han, Dong-Jin and Han, Byung Woo and
   Harris, Todd and Harshbarger, Jayson and Hastings, Robert K. and Hayes,
   Richard D. and Hoede, Claire and Hu, Shen and Hu, Zhi-Liang and
   Hutchins, Lucie and Kan, Zhengyan and Kawaji, Hideya and Keliet, Aminah
   and Kerhornou, Arnaud and Kim, Sunghoon and Kinsella, Rhoda and Klopp,
   Christophe and Kong, Lei and Lawson, Daniel and Lazarevic, Dejan and
   Lee, Ji-Hyun and Letellier, Thomas and Li, Chuan-Yun and Lio, Pietro and
   Liu, Chu-Jun and Luo, Jie and Maass, Alejandro and Mariette, Jerome and
   Maurel, Thomas and Merella, Stefania and Mohamed, Azza Mostafa and
   Moreews, Francois and Nabihoudine, Ibounyamine and Ndegwa, Nelson and
   Noirot, Celine and Perez-Llamas, Cristian and Primig, Michael and
   Quattrone, Alessandro and Quesneville, Hadi and Rambaldi, Davide and
   Reecy, James and Riba, Michela and Rosanoff, Steven and Saddiq, Amna Ali
   and Salas, Elisa and Sallou, Olivier and Shepherd, Rebecca and Simon,
   Reinhard and Sperling, Linda and Spooner, William and Staines, Daniel M.
   and Steinbach, Delphine and Stone, Kevin and Stupka, Elia and Teague,
   Jon W. and Ullah, Abu Z. Dayem and Wang, Jun and Ware, Doreen and
   Wong-Erasmus, Marie and Youens-Clark, Ken and Zadissa, Amonida and
   Zhang, Shi-Jian and Kasprzyk, Arek},
Title = {The BioMart community portal: an innovative alternative to large,
   centralized data repositories},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2015},
Volume = {43},
Number = {W1},
Pages = {W589-W598},
Month = {JUL 1},
Abstract = {The BioMart Community Portal (www.biomart.org) is a community-driven
   effort to provide a unified interface to biomedical databases that are
   distributed worldwide. The portal provides access to numerous database
   projects supported by 30 scientific organizations. It includes over 800
   different biological datasets spanning genomics, proteomics, model
   organisms, cancer data, ontology information and more. All resources
   available through the portal are independently administered and funded
   by their host organizations. The BioMart data federation technology
   provides a unified interface to all the available data. The latest
   version of the portal comes with many new databases that have been
   created by our ever-growing community. It also comes with better support
   and extensibility for data analysis and visualization tools. A new
   addition to our toolbox, the enrichment analysis tool is now accessible
   through graphical and web service interface. The BioMart community
   portal averages over one million requests per day. Building on this
   level of service and the wealth of information that has become
   available, the BioMart Community Portal has introduced a new, more
   scalable and cheaper alternative to the large data stores maintained by
   specialized organizations.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Kasprzyk, A (Corresponding Author), Ist Sci San Raffaele, Ctr Translat Genom \& Bioinformat, Via Olgettina 58, I-20132 Milan, Italy.
   Smedley, Damian; Forbes, Simon; Shepherd, Rebecca; Teague, Jon W., Wellcome Trust Sanger Inst, Hinxton CB10 1SD, England.
   Haider, Syed, Univ Oxford, Weatherall Inst Mol Med, Oxford OX3 9DS, England.
   Durinck, Steffen, Genentech Inc, San Francisco, CA 94080 USA.
   Pandini, Luca; Provero, Paolo; Barbiera, Giulia; Bucci, Gabriele; Buetti, Iwan; Cittaro, Davide; Garcia-Manteiga, Jose M.; Lazarevic, Dejan; Merella, Stefania; Rambaldi, Davide; Riba, Michela; Stupka, Elia; Kasprzyk, Arek, Ist Sci San Raffaele, Ctr Translat Genom \& Bioinformat, I-20132 Milan, Italy.
   Provero, Paolo, Univ Turin, Dept Mol Biotechnol \& Hlth Sci, Turin, Italy.
   Allen, James; Burge, Sarah; Kerhornou, Arnaud; Kinsella, Rhoda; Luo, Jie; Maurel, Thomas; Rosanoff, Steven; Staines, Daniel M.; Zadissa, Amonida, European Bioinformat Inst, European Mol Biol Lab, Cambridge CB10 1SD, England.
   Arnaiz, Olivier; Sperling, Linda, Univ Paris 11, CNRS, CEA, I2BC, F-91198 Gif Sur Yvette, France.
   Awedh, Mohammad Hamza, King Abdulaziz Univ, Fac Engn, Dept Elect \& Comp Engn, Jeddah 21413, Saudi Arabia.
   Baldock, Richard; Haggarty, Bernard, Western Gen Hosp, Inst Genet \& Mol Med, MRC Human Genet Unit, Edinburgh EH4 2XU, Midlothian, Scotland.
   Bardou, Philippe; Cabau, Cedric, Sigenae, INRA, Castanet Tolosan, France.
   Beck, Tim; Brookes, Anthony J.; Chrysostomou, Charalambos; Free, Robert C.; Hastings, Robert K., Univ Leicester, Dept Genet, Leicester LE1 7RH, Leics, England.
   Blake, Andrew, MRC Harwell, Didcot OX11 0RD, Oxon, England.
   Bonierbale, Merideth; Cordova, Raul; Salas, Elisa; Simon, Reinhard, CIP, Lima 1558, Peru.
   Carlson, Joseph W.; Goodstein, David; Hayes, Richard D., Joint Genome Inst, Dept Energy, Walnut Creek, CA USA.
   Chelala, Claude; Cutts, Rosalind J.; Gadaleta, Emanuela; Guerra-Assuncao, JoseE Afonso; Ullah, Abu Z. Dayem, Queen Mary Univ London, Barts Canc Inst, Ctr Mol Oncol, London EC1M 6BQ, England.
   Collin, Olivier; Sallou, Olivier, INRIA, IRISA, F-35042 Rennes, France.
   Dassi, Erik; Quattrone, Alessandro, Univ Trento, Ctr Integrat Biol, Lab Translat Genom, Trento, Italy.
   Di Genova, Alex; Maass, Alejandro, Univ Chile, Ctr Math Modeling, Beauchef 851, Chile.
   Di Genova, Alex; Maass, Alejandro, Univ Chile, Ctr Genome Regulat, Beauchef 851, Chile.
   Djari, Anis; Hoede, Claire; Klopp, Christophe; Mariette, Jerome; Nabihoudine, Ibounyamine; Noirot, Celine, INRA, Plate Forme Bioinformat Genotoul, Math \& Informat Appl Toulouse, F-31326 Castanet Tolosan, France.
   Esposito, Anthony; Estrella, Heather; Fernandez-Banet, Julio; Kan, Zhengyan, Pfizer, Oncol Computat Biol, La Jolla, CA USA.
   Eyras, Eduardo, Passeig Lluis Co, Catalan Inst Res \& Adv Studies ICREA, E-08010 Barcelona, Spain.
   Eyras, Eduardo; Perez-Llamas, Cristian, Univ Pompeu Fabra, E-08003 Barcelona, Spain.
   Fujisawa, Takatomo, Kasuza DNA Res Inst, Chiba 2920818, Japan.
   Gray, Kristian, European Bioinformat Inst EMBL EBI, HUGO Gene Nomenclature Comm HGNC, Hinxton CB10 1SD, England.
   Han, Dong-Jin; Kim, Sunghoon; Lee, Ji-Hyun, Seoul Natl Univ, Coll Pharm, Med Bioconvergence Res Ctr, Seoul 151742, South Korea.
   Han, Dong-Jin; Kim, Sunghoon, Seoul Natl Univ, Dept Mol Med \& Biopharmaceut Sci, Seoul 151742, South Korea.
   Han, Byung Woo; Lee, Ji-Hyun, Seoul Natl Univ, Coll Pharm, Res Inst Pharmaceut Sci, Seoul 151742, South Korea.
   Han, Byung Woo; Lee, Ji-Hyun, Seoul Natl Univ, Informat Ctr Biopharmacol Network, Suwon 443270, South Korea.
   Harris, Todd, Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada.
   Harshbarger, Jayson; Kawaji, Hideya, RIKEN Ctr Life Sci Technol CLST, DGT, Yokohama, Kanagawa 2300045, Japan.
   Hu, Shen, Univ Calif Los Angeles, Sch Dent, Los Angeles, CA 90095 USA.
   Hu, Shen, Univ Calif Los Angeles, Dent Res Inst, Los Angeles, CA 90095 USA.
   Hu, Zhi-Liang; Reecy, James, Iowa State Univ, Iowa City, IA USA.
   Hutchins, Lucie; Stone, Kevin, Jackson Lab, Mouse Genom Informat Grp, Bar Harbor, ME 04609 USA.
   Kawaji, Hideya, RIKEN Prevent Med \& Diag Innovat Program, Wako, Saitama 3510198, Japan.
   Keliet, Aminah; Letellier, Thomas; Quesneville, Hadi; Steinbach, Delphine, INRA URGI Ctr Versailles, F-78026 Versailles, France.
   Kong, Lei; Wang, Jun, Peking Univ, Coll Life Sci, State Key Lab Prot \& Plant Gene Res, Ctr Bioinformat, Beijing 100871, Peoples R China.
   Lawson, Daniel, European Bioinformat Inst, VectorBase, Hinxton CB10 1SD, England.
   Li, Chuan-Yun; Liu, Chu-Jun; Zhang, Shi-Jian, Peking Univ, Inst Mol Med, Beijing 100871, Peoples R China.
   Lio, Pietro, Univ Cambridge, Comp Lab, Cambridge CB3 0FD, England.
   Maass, Alejandro, Univ Chile, Dept Engn Math, Santiago, Chile.
   Mohamed, Azza Mostafa, King Abdulaziz Univ, Fac Sci Girls, Dept Biochem, Jeddah 21413, Saudi Arabia.
   Ndegwa, Nelson, Karolinska Inst, Dept Med Epidemiol \& Biostat, S-17177 Stockholm, Sweden.
   Primig, Michael, Univ Rennes 1, Inserm IRSET U1085, F-35042 Rennes, France.
   Saddiq, Amna Ali, King Abdulaziz Univ, Fac Sci Girls, Dept Biol Sci, Jeddah 21413, Saudi Arabia.
   Spooner, William; Ware, Doreen; Youens-Clark, Ken, Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA.
   Spooner, William, Eagle Genom Ltd, Cambridge CB22 3AT, England.
   Wong-Erasmus, Marie, Human Longev Inc, San Diego, CA 92121 USA.
   Kasprzyk, Arek, King Abdulaziz Univ, Fac Sci, Dept Biol Sci, Jeddah, Saudi Arabia.},
DOI = {10.1093/nar/gkv350},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {BIOINFORMATICS; ACCESS; BIOCONDUCTOR; RESOURCE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {Arek.Kasprzyk@gmail.com},
Affiliations = {Wellcome Trust Sanger Institute; University of Oxford; Roche Holding;
   Genentech; Vita-Salute San Raffaele University; IRCCS Ospedale San
   Raffaele; University of Turin; European Molecular Biology Laboratory
   (EMBL); CEA; Universite Paris Saclay; Centre National de la Recherche
   Scientifique (CNRS); King Abdulaziz University; University of Edinburgh;
   INRAE; University of Leicester; MRC Harwell; CGIAR; International Potato
   Center (CIP); United States Department of Energy (DOE); Joint BioEnergy
   Institute - JBEI; Joint Genome Institute - JGI; University of London;
   Queen Mary University London; Universite de Rennes; Inria; University of
   Trento; Universidad de Chile; Universidad de Chile; INRAE; Pfizer;
   ICREA; Pompeu Fabra University; European Molecular Biology Laboratory
   (EMBL); Seoul National University (SNU); Seoul National University
   (SNU); Seoul National University (SNU); Seoul National University (SNU);
   Ontario Institute for Cancer Research; University of Toronto; RIKEN;
   University of California System; University of California Los Angeles;
   University of California System; University of California Los Angeles;
   Iowa State University; Jackson Laboratory; RIKEN; INRAE; Peking
   University; European Molecular Biology Laboratory (EMBL); Peking
   University; University of Cambridge; Universidad de Chile; King
   Abdulaziz University; Karolinska Institutet; Institut National de la
   Sante et de la Recherche Medicale (Inserm); Universite de Rennes; King
   Abdulaziz University; Cold Spring Harbor Laboratory; King Abdulaziz
   University},
ResearcherID-Numbers = {Riba, Michela/AAG-8955-2019
   mohamed, azza Mostafa/I-5066-2012
   Manteiga, Jose Manuel Garcia/AAN-1954-2020
   Primig, Michael/G-3175-2013
   Lazarevic, Dejan/AAN-1861-2020
   Hu, Steve/B-3799-2011
   P. Lió, Pietro Lio/AAV-3358-2021
   Free, Robert/AAB-1070-2021
   ndegwa, nelson/E-1749-2015
   Eduardo, Eyras/L-1053-2014
   Cittaro, Davide/K-2405-2018
   Maass, Alejandro E/D-5848-2012
   Saddiq, Amna Ali/J-6542-2012
   Provero, Paolo/AAC-1930-2019
   Klopp, Christophe/J-3164-2019
   Allen, James E/B-2457-2009
   Kim, Sunghoon/AAE-8314-2020
   Chrysostomou, Charalambos/F-8707-2010
   Kawaji, Hideya/N-5116-2015
   Smedley, Damian/AAL-8172-2021
   Gasull, Martina/J-4076-2019
   Awedh, Mohammad/P-7168-2014
   QUATTRONE, Aldo/A-6734-2016
   Sperling, Linda/C-9734-2014
   Dassi, Erik/F-6669-2018
   Barbiera, Giulia/AAO-3751-2020
   Eyras, Eduardo/ABG-7144-2020
   Quesneville, Hadi/AAG-1048-2020
   Bucci, Gabriele/H-3002-2014
   Guerra-Assuncao, Jose Afonso/F-3887-2011},
ORCID-Numbers = {Manteiga, Jose Manuel Garcia/0000-0002-5481-040X
   Primig, Michael/0000-0002-2061-0119
   P. Lió, Pietro Lio/0000-0002-0540-5053
   Free, Robert/0000-0001-8053-435X
   ndegwa, nelson/0000-0001-5297-5107
   Eduardo, Eyras/0000-0003-0793-6218
   Cittaro, Davide/0000-0003-0384-3700
   Maass, Alejandro E/0000-0002-7038-4527
   Klopp, Christophe/0000-0001-7126-5477
   Allen, James E/0000-0002-3894-4854
   Chrysostomou, Charalambos/0000-0001-8131-2791
   Kawaji, Hideya/0000-0002-0575-0308
   Awedh, Mohammad/0000-0002-7055-010X
   QUATTRONE, Aldo/0000-0003-2001-957X
   Dassi, Erik/0000-0003-4487-0449
   Barbiera, Giulia/0000-0003-1789-9596
   Eyras, Eduardo/0000-0003-0793-6218
   Quesneville, Hadi/0000-0003-3001-4908
   Wong-Erasmus, Marie/0000-0003-0066-6606
   Kerhornou, Arnaud/0000-0002-2890-295X
   Fernandez Banet, Julio/0000-0003-0901-1286
   Burge, Sarah/0000-0002-2506-927X
   kim, sunghoon/0000-0002-1570-3230
   Baldock, Richard/0000-0003-0332-6877
   Quattrone, Alessandro/0000-0003-3333-7630
   Beck, Tim/0000-0002-0292-7972
   Di Genova, Alex/0000-0002-3120-9283
   Blake, Andrew/0000-0002-8154-6253
   Zadissa, Amonida/0000-0001-5310-8830
   ARNAIZ, Olivier/0000-0002-9626-1015
   Lawson, Daniel/0000-0001-7765-983X
   Maurel, Thomas/0000-0003-0247-3971
   Simon, Reinhard/0000-0002-4608-9077
   Rosanoff, Steven/0000-0002-4216-4674
   Collin, Olivier/0000-0002-8959-8402
   Hayes, Richard/0000-0002-5236-7918
   Bardou, Philippe/0000-0002-0004-0251
   Merella, Stefania/0000-0002-5673-1975
   Goodstein, David/0000-0001-6287-2697
   Saddiq, Amna/0000-0002-8768-8666
   chelala, claude/0000-0002-2488-0669
   Hastings, Robert/0000-0001-8703-127X
   riba, michela/0000-0003-4857-2027
   Mohamed, Azza/0000-0002-8580-2824
   Sperling, Linda/0000-0002-7772-4774
   Lazarevic, Dejan/0000-0003-4527-290X
   Li, Chuan-Yun/0000-0002-8008-8430
   Salas, Elisa/0000-0002-8247-6920
   Hoede, Claire/0000-0001-5054-7731
   Staines, Daniel/0000-0002-7564-9125
   Reecy, James/0000-0003-4602-0990
   Bucci, Gabriele/0000-0001-9838-7204
   Guerra-Assuncao, Jose Afonso/0000-0001-6593-403X},
Funding-Acknowledgement = {Wellcome Trust {[}077012/Z/05/Z, WT095908, WT098051]; Spanish Government
   {[}BIO2011-23920, CSD2009-00080]; Sandra Ibarra Foundation for Cancer
   {[}FSI2013]; Breast Cancer Campaign Tissue Bank {[}09TBBAR]; Office of
   Science of the U.S. Department of Energy {[}DE-AC02-05CH11231]; Global
   Frontier Project - Ministry of Science, ICT and Future Planning through
   National Research Foundation of Korea {[}NRF-2013M3A6A4043695]; Agence
   National de la Recherche {[}ANR-10-BLAN-1122, ANR-12-BSV6-0017-03,
   ANR-14-CE10-0005-03]; Centre National de la Recherche Scientifique;
   Center for Genome Regulation {[}SalmonDB] {[}Fondap-1509007]; Center for
   Mathematical Modelling {[}Basal-PFB 03]; European Molecular Biology
   Laboratory; Japanese Ministry of Education, Culture, Sports, Science and
   Technology {[}FANTOM5 BioMart]; Deanship of Scientific Research (DSR)
   King Abdulaziz University {[}96-130-35-HiCi]; King Abdulaziz University;
   Medical Research Council {[}MC\_PC\_U127527203] Funding Source:
   researchfish; MRC {[}MC\_PC\_U127527203] Funding Source: UKRI; Direct
   For Biological Sciences; Division Of Integrative Organismal Systems
   {[}1127112] Funding Source: National Science Foundation; Agence
   Nationale de la Recherche (ANR) {[}ANR-12-BSV6-0017, ANR-10-BLAN-1122]
   Funding Source: Agence Nationale de la Recherche (ANR); ICREA Funding
   Source: Custom},
Funding-Text = {The BioMart Community Portal is a collaborative, community effort and as
   such it is the product of the efforts of dozens of different groups and
   organizations. The individual data sources that the portal comprises are
   funded separately and independently. In particular: Wellcome Trust
   {[}077012/Z/05/Z to COSMIC mart]; Spanish Government {[}BIO2011-23920
   and CSD2009-00080 to BioMart database of the Regulatory Genomics group
   at Pompeu Fabra University]; Sandra Ibarra Foundation for Cancer
   {[}FSI2013]; Breast Cancer Campaign Tissue Bank {[}09TBBAR to BCCTB
   bioinformatics portal]; Office of Science of the U.S. Department of
   Energy {[}DE-AC02-05CH11231 to Phytozome]; Global Frontier Project (to
   i-Pharm research) funded by the Ministry of Science, ICT and Future
   Planning through the National Research Foundation of Korea
   (NRF-2013M3A6A4043695); Agence National de la Recherche
   {[}ANR-10-BLAN-1122, ANR-12-BSV6-0017-03, ANR-14-CE10-0005-03 to
   ParameciumDB and cilDB]; Centre National de la Recherche Scientifique;
   Center for Genome Regulation {[}SalmonDB; Fondap-1509007 to A.M. and
   A.D.G.]; Center for Mathematical Modelling {[}Basal-PFB 03 to A.M. and
   A.D.G.]; Wellcome Trust (WT095908 and WT098051 to R.K., T.M. and A.Z.);
   European Molecular Biology Laboratory; Japanese Ministry of Education,
   Culture, Sports, Science and Technology {[}FANTOM5 BioMart; for RIKEN
   OSC and RIKEN PMI to Yoshihide Hayashizaki, and for RIKEN CLST].
   Deanship of Scientific Research (DSR) King Abdulaziz University
   (96-130-35-HiCi to M.H.A., A.M.M., A.A.S. and A.K.). Funding for open
   access charge: King Abdulaziz University.},
Number-of-Cited-References = {53},
Times-Cited = {485},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {68},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {CP3IP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000359772700095},
OA = {Green Published, gold, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000290592100009,
Author = {Peters, Dale and Lossau, Norbert},
Title = {DRIVER: building a sustainable infrastructure for global repositories},
Journal = {ELECTRONIC LIBRARY},
Year = {2011},
Volume = {29},
Number = {2},
Pages = {249-260},
Abstract = {Purpose - DRIVER embodies a bold vision that of worldwide networks of
   scientific data repositories. This paper seeks to examine the aims of
   the European Union funded project, to explore the development of a
   distributed infrastructure that enables enhanced interoperability of
   data, resulting in a global knowledge infrastructure supporting the
   scholarly communication of the future.
   Design/methodology/approach - The primary objective of DRIVER was to
   establish a flexible, robust, and scalable infrastructure for all
   European and world-wide digital repositories, managing scientific
   information in an open access model increasingly demanded by
   researchers, funding organisations and other stakeholders. Adopting a
   result-driven approach, activities focused on the expansion of the
   content base with high quality research outputs, including textual
   research papers, data sets and other scholarly publications.
   Findings - The release of the D-NET v1.0 open source software proved a
   successful basis for a distributed service-oriented architecture,
   enabling enhanced interoperability of data and service-providers, and
   offering wide-ranging functionality including search; recommendation;
   collection building, and personal profiling as innovative tools for
   repository managers. In addition, it was found that in building a robust
   network of voluntary content providers, known as the DRIVER
   Confederation, the infrastructure came to support a durable
   organisational structure, now formally constituted as the Confederation
   of Open Access Repositories (COAR). The international repository
   organisation enables further collaboration between research communities
   in a co-ordinated network comprising a growing number of institutional
   repositories, national federations and research institutions and data
   aggregators.
   Practical implications - The development of COAR is the extension of the
   EU-based infrastructure to global research communities in China, India,
   Africa and Latin America, deploying a vigorous awareness and advocacy
   programme. Evolving from the DRIVER Confederation, COAR aims to provide
   an ongoing support service for repository managers, in a dynamic set of
   guidelines aimed at data interoperability, and to provide the strategic
   support required to implement new forms of scholarly communication.
   These issues are addressed in terms of technical infrastructure
   developments but will focus on strategic issues of policy development,
   improved services and additional functionality offered to the scholarly
   community.
   Originality/value - This paper outlines DRIVER's unique response to the
   changing global information environment. Concepts of strategic
   international collaboration are pursued in COAR, based on the scientific
   and technical collaboration achieved in DRIVER. The paper addresses
   significant repository development goals that currently challenge
   repository managers, librarians, scholars and funders and that indicate
   the future of Open Access publication in the ultimate goal of a global
   and interactive representation of human knowledge.},
Publisher = {EMERALD GROUP PUBLISHING LIMITED},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Peters, D (Corresponding Author), Univ Kwazulu Natal, ICT Div, Durban, South Africa.
   Peters, Dale, Univ Kwazulu Natal, ICT Div, Durban, South Africa.
   Lossau, Norbert, Gottingen State \& Univ Lib, Digitisat Ctr, Gottingen, Germany.},
DOI = {10.1108/02640471111125203},
ISSN = {0264-0473},
Keywords = {Open access; Digital storage; Information management; Software tools},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {petersd@ukzn.ac.za},
Affiliations = {University of Kwazulu Natal; University of Gottingen},
ORCID-Numbers = {Peters, Dale/0000-0002-4160-3874},
Number-of-Cited-References = {7},
Times-Cited = {6},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {37},
Journal-ISO = {Electron. Libr.},
Doc-Delivery-Number = {763XD},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000290592100009},
DA = {2024-01-15},
}

@article{ WOS:000608035900011,
Author = {Messinger, Adam and Sirmpilatze, Nikoloz and Heuer, Katja and Loh, Kep
   Kee and Mars, Rogier B. and Sein, Julien and Xu, Ting and Glen, Daniel
   and Jung, Benjamin and Seidlitz, Jakob and Taylor, Paul and Toro,
   Roberto and Garza-Villarreal, Eduardo A. and Sponheim, Caleb and Wang,
   Xindi and Benn, R. Austin and Cagna, Bastien and Dadarwal, Rakshit and
   Evrard, Henry C. and Garcia-Saldivar, Pamela and Giavasis, Steven and
   Hartig, Renee and Lepage, Claude and Liu, Cirong and Majka, Piotr and
   Merchant, Hugo and Milham, Michael P. and Rosa, Marcello G. P. and
   Tasserie, Jordy and Uhrig, Lynn and Margulies, Daniel S. and Klink, P.
   Christiaan},
Title = {A collaborative resource platform for non-human primate neuroimaging},
Journal = {NEUROIMAGE},
Year = {2021},
Volume = {226},
Month = {FEB 1},
Abstract = {Neuroimaging non-human primates (NHPs) is a growing, yet highly
   specialized field of neuroscience. Resources that were primarily
   developed for human neuroimaging often need to be significantly adapted
   for use with NHPs or other animals, which has led to an abundance of
   custom, in-house solutions. In recent years, the global NHP neuroimaging
   community has made significant efforts to transform the field towards
   more open and collaborative practices. Here we present the PRIMatE
   Resource Exchange (PRIME-RE), a new collaborative online platform for
   NHP neuroimaging. PRIME-RE is a dynamic community-driven hub for the
   exchange of practical knowledge, specialized analytical tools, and open
   data repositories, specifically related to NHP neuroimaging. PRIME-RE
   caters to both researchers and developers who are either new to the
   field, looking to stay abreast of the latest developments, or seeking to
   collaboratively advance the field},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Klink, PC (Corresponding Author), Netherlands Inst Neurosci, Dept Vis \& Cognit, Amsterdam, Netherlands.
   Messinger, Adam; Jung, Benjamin, NIMH, Lab Brain \& Cognit, Bethesda, MD 20892 USA.
   Sirmpilatze, Nikoloz; Dadarwal, Rakshit, Leibniz Inst Primate Res, German Primate Ctr, Kellnerweg 4, D-37077 Gottingen, Germany.
   Sirmpilatze, Nikoloz; Dadarwal, Rakshit, Georg August Univ Gottingen, D-37073 Gottingen, Germany.
   Heuer, Katja, Max Planck Inst Human Cognit \& Brain Sci, Leipzig, Germany.
   Heuer, Katja; Toro, Roberto, Univ Paris, Ctr Res \& Interdisciplinar CRI, INSERM U1284, Paris, France.
   Loh, Kep Kee; Sein, Julien; Cagna, Bastien, Aix Marseille Univ, Inst Neurosci Timone INT, CNRS, UMR 7289, F-13005 Marseille, France.
   Loh, Kep Kee, Aix Marseille Univ, Inst Language Commun \& Brain, Marseille, France.
   Mars, Rogier B., Univ Oxford, John Radcliffe Hosp, Nuffield Dept Clin Neurosci, Wellcome Ctr Integrat Neuroimaging, Oxford OX3 9DU, England.
   Mars, Rogier B., Radboud Univ Nijmegen, Donders Inst Brain Cognit \& Behav, Montessorilaan 3, NL-6525 HR Nijmegen, Netherlands.
   Xu, Ting; Giavasis, Steven; Milham, Michael P., Child Mind Inst, 101 E 56th St, New York, NY 10022 USA.
   Glen, Daniel; Taylor, Paul, NIMH, Sci \& Stat Comp Core, Bethesda, MD 20892 USA.
   Jung, Benjamin, Brown Univ, Dept Neurosci, Providence, RI 02912 USA.
   Seidlitz, Jakob, Childrens Hosp Philadelphia, Dept Child \& Adolescent Psychiat \& Behav Sci, Philadelphia, PA 19104 USA.
   Seidlitz, Jakob, Univ Penn, Dept Psychiat, Philadelphia, PA 19104 USA.
   Toro, Roberto, Univ Paris, CNRS, UMR 3571, Dept Neurosci,Inst Pasteur, Paris, France.
   Garza-Villarreal, Eduardo A.; Garcia-Saldivar, Pamela; Merchant, Hugo, Univ Nacl Autonoma Mexico, Inst Neurobiol, Campus Juriquilla, Queretaro, Mexico.
   Sponheim, Caleb, Univ Chicago, Dept Organismal Biol \& Anat, Chicago, IL 60637 USA.
   Wang, Xindi; Lepage, Claude, Montreal Neurol Inst MNI, McGill Ctr Integrat Neurosci, Montreal, PQ, Canada.
   Benn, R. Austin, Ctr Nacl Invest Cardiovasc Carlos III CNIC, Madrid, Spain.
   Evrard, Henry C.; Hartig, Renee, Univ Tubingen, Ctr Integrat Neurosci, Tubingen, Germany.
   Evrard, Henry C.; Hartig, Renee, Max Planck Inst Biol Cybernet, Tubingen, Germany.
   Evrard, Henry C.; Milham, Michael P., Nathan S Kline Inst Psychiat Res, Orangeburg, NY 10962 USA.
   Evrard, Henry C., Chinese Acad Sci, Int Ctr Primate Brain Res, Shanghai, Peoples R China.
   Hartig, Renee, Univ Med Ctr, Focus Program Translat Neurosci, Mainz, Germany.
   Liu, Cirong, Univ Pittsburgh, Dept Neurobiol, Brain Inst, Pittsburgh, PA USA.
   Majka, Piotr, Polish Acad Sci, Nencki Inst Expt Biol, Lab Neuroinformat, PL-02093 Warsaw, Poland.
   Majka, Piotr; Rosa, Marcello G. P., Monash Univ Node, Ctr Excellence Integrat Brain Funct, Australian Res Council, Clayton, Vic 3800, Australia.
   Majka, Piotr; Rosa, Marcello G. P., Monash Univ, Biomed Discovery Inst, Clayton, Vic 3800, Australia.
   Majka, Piotr; Rosa, Marcello G. P., Monash Univ, Dept Physiol, Clayton, Vic 3800, Australia.
   Tasserie, Jordy; Uhrig, Lynn, NeuroSpin Ctr, Direct Rech Fondamentale, Commissariat Energie Atom \& Energies Alternat, Gif Sur Yvette, France.
   Tasserie, Jordy; Uhrig, Lynn, Inst Natl Sante \& Rech Med U992, Cognit Neuroimaging Unit, Gif Sur Yvette, France.
   Tasserie, Jordy, Univ Paris Saclay, Paris, France.
   Margulies, Daniel S., Ctr Natl Rech Sci CNRS, UMR 8002, Integrat Neurosci \& Cognit Ctr, Paris, France.
   Klink, P. Christiaan, Netherlands Inst Neurosci, Dept Vis \& Cognit, Amsterdam, Netherlands.},
DOI = {10.1016/j.neuroimage.2020.117519},
Article-Number = {117519},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords = {Open science; Resource sharing; Toolbox; Pipeline; Structural;
   Functional; Diffusion},
Keywords-Plus = {DIFFUSION TRACTOGRAPHY; DIFFEOMORPHIC REGISTRATION; MOTION CORRECTION;
   BRAIN; MONKEY; ATLAS; VISUALIZATION; OPTIMIZATION; MARMOSET; TOOLS},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {C.Klink@nin.knaw.nl},
Affiliations = {National Institutes of Health (NIH) - USA; NIH National Institute of
   Mental Health (NIMH); Deutsches Primatenzentrum (DPZ); University of
   Gottingen; Max Planck Society; Universite Paris Cite; Centre National de
   la Recherche Scientifique (CNRS); CNRS - National Institute for Biology
   (INSB); Aix-Marseille Universite; Assistance Publique-Hopitaux de
   Marseille; Aix-Marseille Universite; University of Oxford; Radboud
   University Nijmegen; National Institutes of Health (NIH) - USA; NIH
   National Institute of Mental Health (NIMH); Brown University; University
   of Pennsylvania; Pennsylvania Medicine; Childrens Hospital of
   Philadelphia; University of Pennsylvania; Le Reseau International des
   Instituts Pasteur (RIIP); Universite Paris Cite; Institut Pasteur Paris;
   Centre National de la Recherche Scientifique (CNRS); CNRS - National
   Institute for Biology (INSB); Universidad Nacional Autonoma de Mexico;
   University of Chicago; Centro Nacional de Investigaciones
   Cardiovasculares (CNIC); Eberhard Karls University of Tubingen; Max
   Planck Society; Nathan Kline Institute for Psychiatric Research; Chinese
   Academy of Sciences; Johannes Gutenberg University of Mainz;
   Pennsylvania Commonwealth System of Higher Education (PCSHE); University
   of Pittsburgh; Polish Academy of Sciences; Nencki Institute of
   Experimental Biology of the Polish Academy of Sciences; Monash
   University; Monash University; Monash University; CEA; Universite Paris
   Saclay; CEA; Universite Paris Saclay; Universite Paris Saclay;
   Universite Paris Cite; Centre National de la Recherche Scientifique
   (CNRS); Royal Netherlands Academy of Arts \& Sciences; Netherlands
   Institute for Neuroscience (NIN-KNAW)},
ResearcherID-Numbers = {Wang, Xindi/JKP-9602-2023
   Garza-Villarreal, Eduardo/A-7879-2008
   Merchant, Hugo/E-8703-2019
   Heuer, Katja/AAJ-2594-2020
   Mars, Rogier/G-2312-2018
   Milham, Michael P./Y-3160-2019
   TASSERIE, Jordy/HQY-2603-2023
   Mars, Rogier/GWZ-9665-2022
   Majka, Piotr/P-9741-2016
   Seidlitz, Jakob/K-9360-2019
   Glen, Daniel/HCG-8456-2022
   Rosa, Marcello/D-9278-2013
   },
ORCID-Numbers = {Garza-Villarreal, Eduardo/0000-0003-1381-8648
   Merchant, Hugo/0000-0002-3488-9501
   Heuer, Katja/0000-0002-7237-0196
   Mars, Rogier/0000-0001-6302-8631
   Majka, Piotr/0000-0002-9055-8686
   Seidlitz, Jakob/0000-0002-8164-7476
   Rosa, Marcello/0000-0002-6620-6285
   Evrard, Henry/0000-0001-8429-4699
   Jung, Benjamin/0000-0002-8906-8452
   Loh, Kep Kee/0000-0003-0650-224X
   Glen, Daniel/0000-0001-8456-5647
   Sirmpilatze, Nikoloz/0000-0003-1778-2427
   Messinger, Adam/0000-0002-8939-7897
   Toro, Roberto/0000-0002-6671-858X
   TASSERIE, Jordy/0000-0001-9626-7823},
Funding-Acknowledgement = {Intramural Research Program of the NIMH; Fondation pour la Recherche
   Medicale (FRM grant) {[}ECO20160736100]; Fondation de France, Human
   Brain Project; Biotechnology and Biological Sciences Research Council
   (BBSRC) UK {[}BB/N019814/1]; Wellcome Trust {[}203129/Z/16/Z]; 
   {[}ANR-19-DATA-0025-01]; BBSRC {[}BB/N019814/1] Funding Source: UKRI},
Funding-Text = {We would like to thank Patrick Markwalter for assistance with compiling
   references, editing and formatting. We thank the following people for
   their contributions to shared resources: Richard C. Reynolds, Gang Chen,
   and Robert Cox (AFNI, esp. afni\_proc.py); Konrad Wagstyl and Alan C.
   Evans (CIVET); Leslie Ungerleider (CIVET, NMT); Cameron Craddock
   (C-PAC); David Meunier and Regis Trapeau (Macapype); Jochen Weber
   (NeuroElf); Jonathan Williford (NHP-BIDS); Borja Ibanez (precon\_all);
   Arun Garimella, Felipe Mendez, and Luis Concha (PREEMACS); Antoine
   Grigis and Bechir Jarraya (Pypreclin); Gabriel Devenyi, Nikos K.
   Logothetis, and George Paxinos (SARM);Afonso Silva and David Leopold
   (MBM); Lennart Verhagen and members of the Cognitive Neuroecology Lab
   (MrCat). This research was supported in part by the Intramural Research
   Program of the NIMH and utilized the computational resources of the NIH
   HPC Biowulf cluster (http://hpc.nih.gov).Pypreclin work was supported by
   the Fondation pour la Recherche Medicale (FRM grant number
   ECO20160736100 to JT), Fondation de France, Human Brain Project
   (Corticity project). RT and KH are supported by ANR-19-DATA-0025-01
   NeuroWebLab. RBM is supported by the Biotechnology and Biological
   Sciences Research Council (BBSRC) UK {[}BB/N019814/1]. The Wellcome
   Centre for Integrative Neuroimaging is supported by core funding from
   the Wellcome Trust {[}203129/Z/16/Z].},
Number-of-Cited-References = {96},
Times-Cited = {21},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {PS6KQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000608035900011},
OA = {Green Published, Green Accepted, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000580592500009,
Author = {Boateng, Samuel and Lee, Kwang Ryeol and Deepika and Cho, Haneol and
   Lee, Kyu Hwan and Kim, Chansoo},
Title = {KIST-NOMAD - a Repository to Manage Large Amounts of Computational
   Materials Science Data},
Journal = {KOREAN JOURNAL OF METALS AND MATERIALS},
Year = {2020},
Volume = {58},
Number = {10},
Pages = {728-739},
Month = {OCT},
Abstract = {We introduce the Korea Institute of Science and Technology-Novel
   Materials Discovery (KIST-NOMAD) platform, a materials data repository.
   We describe its functionality and novel features from an academic
   viewpoint. It is a data repository designed for computational material
   science, especially focusing on managing and sharing the results of
   molecular dynamics simulation results as well as quantum mechanical
   computations. It consists of three main components: a database, file
   storage, and web-based front end. The database hosts material
   properties, which are extracted from the computational results. The
   front end has a graphical user interface and an open application
   programming interface, which allow researchers to interact with the
   system more easily. KIST-NOMAD's panel displays the searched results on
   a well-organized and research-oriented web page. All the open access
   data and files are available for downloading in comma-separated value
   format as well as zipped archives. This automated extraction function
   was developed by utilizing database parsers and JSON scripts. KIST-NOMAD
   also has an efficient option to download simulation and computation
   results on a large-scale. All of the above functions are designed to
   satisfy academic and research demands, and make high-throughput
   screening available, while incorporating machine learning for
   computational material engineering. We finally stress that the
   repository platform is user-driven and user-friendly. It is clearly
   designed to follow the modern big-data architecture and re-use
   principles for scientific data, such as being findable, accessible, and
   interoperable.},
Publisher = {KOREAN INST METALS MATERIALS},
Address = {KIM BLDG 6TH FLOOR, SEOCHO-DAERO 56 GIL 38, SEOCHO-GU, SEOUL 137-881,
   SOUTH KOREA},
Type = {Article},
Language = {English},
Affiliation = {Kim, C (Corresponding Author), Korea Inst Sci \& Technol, Computat Sci Res Ctr, Seoul 02792, South Korea.
   Lee, KH (Corresponding Author), Korea Inst Sci \& Technol, Innovat Enterprise Cooperat Ctr, Seoul 02792, South Korea.
   Boateng, Samuel, Univ Sci \& Technol, Dept Nanomat Sci \& Engn, Daejeon 34113, South Korea.
   Lee, Kwang Ryeol; Deepika; Cho, Haneol; Kim, Chansoo, Korea Inst Sci \& Technol, Computat Sci Res Ctr, Seoul 02792, South Korea.
   Boateng, Samuel; Lee, Kyu Hwan, Korea Inst Sci \& Technol, Innovat Enterprise Cooperat Ctr, Seoul 02792, South Korea.},
DOI = {10.3365/KJMM.2020.58.10.728},
ISSN = {1738-8228},
Keywords = {repository for computational material science; open-access data sharing;
   scientific data; data extraction},
Keywords-Plus = {METALS},
Research-Areas = {Materials Science; Metallurgy \& Metallurgical Engineering},
Web-of-Science-Categories  = {Materials Science, Multidisciplinary; Metallurgy \& Metallurgical
   Engineering},
Author-Email = {biometal@kist.re.kr
   eau@kist.re.kr},
Affiliations = {University of Science \& Technology (UST); Korea Institute of Science \&
   Technology (KIST); Korea Institute of Science \& Technology (KIST)},
ResearcherID-Numbers = {Boateng, Samuel/AAX-5135-2021},
ORCID-Numbers = {Boateng, Samuel/0000-0002-0307-3286},
Funding-Acknowledgement = {KIST's Future Convergence Research {[}2E30460]; Ministry of Science and
   ICT's Material Platform Research {[}2N57370]},
Funding-Text = {The authors acknowledge the support of Prof. Matthias Scheffler and the
   FHI theory group for their immense assistance and providing the
   repository data and files. Our research is supported by KIST's Future
   Convergence Research 2E30460 and Ministry of Science and ICT's Material
   Platform Research 2N57370.},
Number-of-Cited-References = {32},
Times-Cited = {2},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Korean J. Met. Mater.},
Doc-Delivery-Number = {OE5TK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000580592500009},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000485301100001,
Author = {da Costa, Michelli Pereira and Lima Leite, Fernando Cesar},
Title = {Factors influencing research data communication on Zika virus: a
   grounded theory},
Journal = {JOURNAL OF DOCUMENTATION},
Year = {2019},
Volume = {75},
Number = {5},
Pages = {910-926},
Month = {SEP 9},
Abstract = {Purpose The purpose of this paper is to propose a theoretical model to
   illustrate factors influencing research data communication on diseases
   caused by the Zika virus. Design/methodology/approach The grounded
   theory methodology was adopted. For data collection, interviews were
   conducted with 13 Brazilian researchers involved with the Zika virus
   theme. Data analysis was performed using the open, axial and selective
   coding processes, according to the principles of the grounded theory.
   Findings Based on data collection and analysis, seven theoretical
   categories representing intervening factors in Zika virus research data
   communication were identified. The emerging theory showed the centrality
   of researchers' expectations for acknowledgment and reward, influenced
   by the aspects of research funding and academic culture. Three factors
   involved in the macro processes of research data communication: data
   use, data production and data sharing. In the use and production
   processes, factors related to collaboration figured most strongly. In
   the production and sharing processes, the factors regarding data
   processing and the use of research data repositories were more
   pronounced. Finally, data sharing, and the possibility of reusing data
   are directly affected by the social context of Zika virus disease as an
   emerging disease. Originality/value The study presents a theory
   developed systematically to explain the phenomenon of communication of
   research data on Zika virus. The theory presents a set of intervening
   factors of the process of communication of research data and discusses
   the factors in light of the fundamentals of information science.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {da Costa, MP (Corresponding Author), Univ Brasilia, Fac Informat Sci, Brasilia, DF, Brazil.
   da Costa, Michelli Pereira; Lima Leite, Fernando Cesar, Univ Brasilia, Fac Informat Sci, Brasilia, DF, Brazil.},
DOI = {10.1108/JD-05-2018-0071},
ISSN = {0022-0418},
EISSN = {1758-7379},
Keywords = {Research data; Scientific communication; Open data; Data sharing; Open
   science; Academic culture; Data communication},
Keywords-Plus = {RESEARCH DATA-MANAGEMENT; TRANSMISSION; INFORMATION; POLICIES},
Research-Areas = {Computer Science; Information Science \& Library Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Information Science \& Library
   Science},
Author-Email = {michellicosta11@gmail.com},
Affiliations = {Universidade de Brasilia},
ResearcherID-Numbers = {Leite, Fernando César Lima/F-9578-2010},
ORCID-Numbers = {Leite, Fernando César Lima/0000-0003-1998-2385},
Number-of-Cited-References = {47},
Times-Cited = {8},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {61},
Journal-ISO = {J. Doc.},
Doc-Delivery-Number = {IW9GI},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000485301100001},
OA = {Green Submitted, Green Published, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000672775800024,
Author = {Zheng, Shuyu and Aldahdooh, Jehad and Shadbahr, Tolou and Wang, Yinyin
   and Aldahdooh, Dalal and Bao, Jie and Wang, Wenyu and Tang, Jing},
Title = {DrugComb update: a more comprehensive drug sensitivity data repository
   and analysis portal},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2021},
Volume = {49},
Number = {W1},
Pages = {W174-W184},
Month = {JUL 2},
Abstract = {Combinatorial therapies that target multiple pathways have shown great
   promises for treating complex diseases. DrugComb (https://drugcomb.org/)
   is a web-based portal for the deposition and analysis of drug
   combination screening datasets. Since its first release, DrugComb has
   received continuous updates on the coverage of data resources, as well
   as on the functionality of the web server to improve the analysis,
   visualization and interpretation of drug combination screens. Here, we
   report significant updates of DrugComb, including: (i) manual curation
   and harmonization of more comprehensive drug combination and monotherapy
   screening data, not only for cancers but also for other diseases such as
   malaria and COVID-19; (ii) enhanced algorithms for assessing the
   sensitivity and synergy of drug combinations; (iii) network modelling
   tools to visualize the mechanisms of action of drugs or drug
   combinations for a given cancer sample and (iv) state-of-the-art machine
   learning models to predict drug combination sensitivity and synergy.
   These improvements have been provided with more user-friendly graphical
   interface and faster database infrastructure, which make DrugComb the
   most comprehensive web-based resources for the study of drug
   sensitivities for multiple diseases.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Tang, J (Corresponding Author), Univ Helsinki, Fac Med, Res Program Syst Oncol, FI-00290 Helsinki, Finland.
   Zheng, Shuyu; Aldahdooh, Jehad; Shadbahr, Tolou; Wang, Yinyin; Aldahdooh, Dalal; Bao, Jie; Wang, Wenyu; Tang, Jing, Univ Helsinki, Fac Med, Res Program Syst Oncol, FI-00290 Helsinki, Finland.
   Bao, Jie, Univ Helsinki, Inst Mol Med Finland, FI-00290 Helsinki, Finland.},
DOI = {10.1093/nar/gkab438},
EarlyAccessDate = {JUN 2021},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {SYNERGY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {jing.tang@helsinki.fi},
Affiliations = {University of Helsinki; University of Helsinki},
ResearcherID-Numbers = {Aldahdooh, Jehad/AAJ-9026-2021
   Tang, Jing/H-4084-2012
   Tang, Jing/W-1764-2019
   Zheng, Shuyu/AAH-2648-2021
   Wang, Yin/HCI-9352-2022
   tang, jing/HHR-9815-2022
   Bao, Jie/C-2452-2019
   },
ORCID-Numbers = {Aldahdooh, Jehad/0000-0002-9947-4067
   Tang, Jing/0000-0001-7480-7710
   Tang, Jing/0000-0001-7480-7710
   Zheng, Shuyu/0000-0003-0624-8077
   Bao, Jie/0000-0002-1993-7309
   Shadbahr, tolou/0000-0001-5715-5933},
Funding-Acknowledgement = {European Research Council (ERC) {[}716063]; European Commission
   {[}824087]; Academy of Finland {[}317680]; Sigrid Juselius Foundation;
   ERC starting grant DrugComb; University of Helsinki through Doctoral
   Program of Biomedicine (DPBM); K. Albin Johanssons stiftelse; Academy of
   Finland (AKA) {[}317680] Funding Source: Academy of Finland (AKA)},
Funding-Text = {European Research Council (ERC) starting grant DrugComb (Informatics
   approaches for the rational selection of personalized cancer drug
   combinations) {[}716063]; European Commission H2020 EOSC-life (Providing
   an open collaborative space for digital biology in Europe {[}824087];
   Academy of FinlandResearch Fellowgrant {[}317680]; Sigrid Jus ` elius
   Foundation. Funding for open access charge: ERC starting grant DrugComb.
   WW and JB hold salaried positions funded by University of Helsinki
   through Doctoral Programof Biomedicine (DPBM); W.W. also receives a
   personal grant from K. Albin Johanssons stiftelse.},
Number-of-Cited-References = {51},
Times-Cited = {32},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {17},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {TI4NF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000672775800024},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000449618200011,
Author = {Forrester, Tavis and O'Brien, Tim and Fegraus, Eric and Jansen, Patrick
   A. and Palmer, Jonathan and Kays, Roland and Ahumada, Jorge and Stern,
   Beth and McShea, William},
Title = {An Open Standard for Camera Trap Data},
Journal = {BIODIVERSITY DATA JOURNAL},
Year = {2016},
Volume = {4},
Abstract = {Camera traps that capture photos of animals are a valuable tool for
   monitoring biodiversity. The use of camera traps is rapidly increasing
   and there is an urgent need for standardization to facilitate data
   management, reporting and data sharing. Here we offer the Camera Trap
   Metadata Standard as an open data standard for storing and sharing
   camera trap data, developed by experts from a variety of organizations.
   The standard captures information necessary to share data between
   projects and offers a foundation for collecting the more detailed data
   needed for advanced analysis. The data standard captures information
   about study design, the type of camera used, and the location and
   species names for all detections in a standardized way. This information
   is critical for accurately assessing results from individual camera
   trapping projects and for combining data from multiple studies for
   meta-analysis. This data standard is an important step in aligning
   camera trapping surveys with best practices in data-intensive science.
   Ecology is moving rapidly into the realm of big data, and central data
   repositories are becoming a critical tool and are emerging for camera
   trap data. This data standard will help researchers standardize data
   terms, align past data to new repositories, and provide a framework for
   utilizing data across repositories and research projects to advance
   animal ecology and conservation.},
Publisher = {PENSOFT PUBLISHERS},
Address = {12 PROF GEORGI ZLATARSKI ST, SOFIA, 1700, BULGARIA},
Type = {Article},
Language = {English},
Affiliation = {Forrester, T (Corresponding Author), Smithsonian Conservat Biol Inst, Front Royal, VA 22630 USA.
   Forrester, T (Corresponding Author), Oregon Dept Fish \& Wildlife, La Grande, OR 97850 USA.
   Forrester, Tavis; McShea, William, Smithsonian Conservat Biol Inst, Front Royal, VA 22630 USA.
   Forrester, Tavis, Oregon Dept Fish \& Wildlife, La Grande, OR 97850 USA.
   O'Brien, Tim; Palmer, Jonathan, Wildlife Conservat Soc, New York, NY USA.
   Fegraus, Eric; Ahumada, Jorge, Conservat Int, Arlington, VA USA.
   Jansen, Patrick A., Smithsonian Trop Res Inst, Balboa, Panama.
   Jansen, Patrick A., Wageningen Univ, Wageningen, Netherlands.
   Kays, Roland, North Carolina State Univ, Raleigh, NC 27695 USA.
   Kays, Roland, North Carolina Museum Nat Sci, Raleigh, NC USA.
   Stern, Beth, Smithsonian Data Ctr, Herndon, VA USA.},
DOI = {10.3897/BDJ.4.e10197},
Article-Number = {e10197},
ISSN = {1314-2836},
EISSN = {1314-2828},
Keywords = {big data; biodiversity; camera trap; data repository; data schema},
Keywords-Plus = {MANAGEMENT; SOFTWARE},
Research-Areas = {Biodiversity \& Conservation},
Web-of-Science-Categories  = {Biodiversity Conservation},
Author-Email = {tavis.d.forrester@state.or.us},
Affiliations = {Smithsonian Institution; Smithsonian National Zoological Park \&
   Conservation Biology Institute; Wildlife Conservation Society;
   Conservation International; Smithsonian Institution; Smithsonian
   Tropical Research Institute; Wageningen University \& Research; North
   Carolina State University},
ResearcherID-Numbers = {Jansen, Patrick A/G-2545-2015
   Ahumada, Jorge/JPX-5713-2023
   },
ORCID-Numbers = {Jansen, Patrick A/0000-0002-4660-0314
   McShea, William/0000-0002-8102-0200
   Kays, Roland/0000-0002-2947-6665},
Funding-Acknowledgement = {National Science Foundation {[}1232442]; Gordon and Betty Moore
   Foundation; Direct For Biological Sciences; Emerging Frontiers
   {[}1550911] Funding Source: National Science Foundation},
Funding-Text = {National Science Foundation Grant \#1232442 and the Gordon and Betty
   Moore Foundation.},
Number-of-Cited-References = {19},
Times-Cited = {29},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {27},
Journal-ISO = {Biodiver. Data J.},
Doc-Delivery-Number = {VH0GB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000449618200011},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000771996800006,
Author = {Quay, Amanda N. and Fiske, Peter S. and Mauter, Meagan S.},
Title = {Recommendations for Advancing FAIR and Open Data Standards in the Water
   Treatment Community},
Journal = {ACS ES\&T ENGINEERING},
Year = {2022},
Volume = {2},
Number = {3},
Pages = {337-346},
Month = {MAR 11},
Abstract = {Water treatment researchers will maximize insights from data by
   implementing FAIR and Open (FAIR/O) principles for data storage and
   management. Progress toward domain-specific FAIR/O data infrastructure
   and practices advance data synthesizability, data extensibility, and
   stakeholder diversity. Embracing FAIR/O data principles in domain
   research would enable datadriven research breakthroughs that benefit a
   diverse array of water treatment research stakeholders. These
   breakthroughs arise from increased data density to improve research
   scope, better crossmode data translation between experimental and
   modeling research outputs, and improved multiscale data integration to
   answer key questions across research scales. This paper addresses the
   gap between the current state of data sharing and the envisioned
   potential of FAIR/O data by offering practical steps toward building
   effective and sustainable water treatment data infrastructure, engaging
   key stakeholders, and motivating their participation. We clarify
   essential activities of a water treatment research data repository and
   suggest opportunities for communicating and growing its value.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Mauter, MS (Corresponding Author), Stanford Univ, Dept Civil \& Environm Engn, Stanford, CA 94305 USA.
   Quay, Amanda N.; Mauter, Meagan S., Stanford Univ, Dept Civil \& Environm Engn, Stanford, CA 94305 USA.
   Fiske, Peter S., Lawrence Berkeley Natl Lab, Natl Alliance Water Innovat, Berkeley, CA 94720 USA.},
DOI = {10.1021/acsestengg.1c00245},
EISSN = {2690-0645},
Keywords = {data; informatics; accessibility; interoperability; reusability},
Keywords-Plus = {DATA-DRIVEN; ELECTROKINETIC TRANSPORT; MULTISCALE MODEL; SYSTEMS;
   METAANALYSIS; NETWORKS; SCIENCE; PORES},
Research-Areas = {Engineering},
Web-of-Science-Categories  = {Engineering, Environmental},
Author-Email = {mauter@stanford.edu},
Affiliations = {Stanford University; United States Department of Energy (DOE); Lawrence
   Berkeley National Laboratory},
ORCID-Numbers = {Mauter, Meagan/0000-0002-4932-890X},
Funding-Acknowledgement = {National Alliance for Water Innovation (NAWI) - U.S. Department of
   Energy, Office of Energy Efficiency and Renewable Energy (EERE),
   Advanced Manufacturing Office {[}DEFOA-0001905]; National Science
   Foundation Graduate Research Fellowship {[}DGE-1656518]; U.S. Department
   of Energy I-Corps program},
Funding-Text = {This material is based upon work supported by the National Alliance for
   Water Innovation (NAWI), funded by the U.S. Department of Energy, Office
   of Energy Efficiency and Renewable Energy (EERE), Advanced Manufacturing
   Office, under Funding Opportunity Announcement Number DEFOA-0001905.
   A.N.Q. also acknowledges support from the National Science Foundation
   Graduate Research Fellowship under Grant No. (DGE-1656518). A.N.Q. and
   P.S.F. gratefully acknowledge the U.S. Department of Energy I-Corps
   program for stakeholder interview training and facilitation and thank J.
   Huggins (NREL) for his I-Corps team contributions.},
Number-of-Cited-References = {74},
Times-Cited = {4},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {ACS ES\&T Eng.},
Doc-Delivery-Number = {ZX6HZ},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000771996800006},
DA = {2024-01-15},
}

@article{ WOS:000793362100001,
Author = {Page, Matthew J. and Phi-Yen Nguyen and Hamilton, Daniel G. and
   Haddaway, Neal R. and Kanukula, Raju and Moher, David and McKenzie,
   Joanne E.},
Title = {Data and code availability statements in systematic reviews of
   interventions were often missing or inaccurate: a content analysis},
Journal = {JOURNAL OF CLINICAL EPIDEMIOLOGY},
Year = {2022},
Volume = {147},
Pages = {1-10},
Month = {JUL},
Abstract = {Objectives: To estimate the frequency of data and code availability
   statements in a random sample of systematic reviews with metaanalysis of
   aggregate data, summarize the content of the statements and investigate
   how often data and code files were shared. Methods: We searched for
   systematic reviews with meta-analysis of aggregate data on the effects
   of a health, social, behavioral, or educational intervention that were
   indexed in PubMed, Education Collection via ProQuest, Scopus via
   Elsevier, or Social Sciences Citation Index and Science Citation Index
   Expanded via Web of Science during a 4-week period (between November 2,
   and December 2, 2020). Records were randomly sorted and screened
   independently by two authors until our target sample of 300 systematic
   reviews was reached. Two authors independently recorded whether a data
   or code availability statement (or both) appeared in each review and
   coded the content of the statements using an inductive approach.
   Results: Of the 300 included systematic reviews with meta-analysis, 86
   (29\%) had a data availability statement, and seven (2\%) had both a
   data and code availability statement. In 12/93 (13\%) data availability
   statements, authors stated that data files were available for download
   from the journal website or a data repository, which we verified as
   being true. While 39/93 (42\%) authors stated data were available upon
   request, 37/93 (40\%) implied that sharing of data files was not
   necessary or applicable to them, most often because ``all data appear in
   the article{''}or ``no datasets were generated or analyzed{''}.
   Discussion: Data and code availability statements appear infrequently in
   systematic review manuscripts. Authors who do provide a data
   availability statement often incorrectly imply that data sharing is not
   applicable to systematic reviews. Our results suggest the need for
   various interventions to increase data and code sharing by systematic
   reviewers. (c) 2022 Elsevier Inc. All rights reserved.},
Publisher = {ELSEVIER SCIENCE INC},
Address = {STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA},
Type = {Review},
Language = {English},
Affiliation = {Page, MJ (Corresponding Author), Monash Univ, Sch Publ Hlth \& Prevent Med, 553 St Kilda Rd, Melbourne, Vic 3004, Australia.
   Page, Matthew J.; Phi-Yen Nguyen; Kanukula, Raju; McKenzie, Joanne E., Monash Univ, Sch Publ Hlth \& Prevent Med, 553 St Kilda Rd, Melbourne, Vic 3004, Australia.
   Hamilton, Daniel G., Univ Melbourne, Sch BioSci, Melbourne, Vic, Australia.
   Haddaway, Neal R., Leibniz Ctr Agr Landscape Res ZALF, Eberswalder Str 84, Muncheberg, Germany.
   Haddaway, Neal R., Stockholm Environm Inst, Linnegatan 87D, Stockholm, Sweden.
   Haddaway, Neal R., Univ Johannesburg, African Ctr Evidence, Johannesburg, South Africa.
   Moher, David, Ottawa Hosp, Ctr Journalol, Clin Epidemiol Program, Res Inst, Ottawa, ON, Canada.
   Moher, David, Univ Ottawa, Fac Med, Sch Epidemiol \& Publ Hlth, Ottawa, ON, Canada.},
DOI = {10.1016/j.jclinepi.2022.03.003},
EarlyAccessDate = {APR 2022},
ISSN = {0895-4356},
EISSN = {1878-5921},
Keywords = {Evidence synthesis; Open synthesis; Open science; Open data;
   Reproducibility of research; Research integrity},
Research-Areas = {Health Care Sciences \& Services; Public, Environmental \& Occupational
   Health},
Web-of-Science-Categories  = {Health Care Sciences \& Services; Public, Environmental \& Occupational
   Health},
Author-Email = {matthew.page@monash.edu},
Affiliations = {Monash University; University of Melbourne; Leibniz Zentrum fur
   Agrarlandschaftsforschung (ZALF); Stockholm Environment Institute;
   University of Johannesburg; University of Ottawa; Ottawa Hospital
   Research Institute; University of Ottawa},
ORCID-Numbers = {Nguyen, Phi-Yen/0000-0002-0476-3385
   Hamilton, Daniel George/0000-0001-8104-474X},
Funding-Acknowledgement = {Australian Research Council Discovery Early Career Researcher Award
   {[}DE200101618]; Australian Commonwealth Government Research Training
   Program Scholarship - Alexander von Hum-boldt Experienced Researcher
   Fellowship; Monash Graduate Scholarship; Monash International Tuition
   Scholarship; University Research Chair, University of Ottawa; National
   Health and Medical Research Council Career Development Fellowship
   {[}APP1143429]; Alexander von Hum-boldt Experienced Researcher
   Fellowship},
Funding-Text = {This research was funded by an Australian Research Council Discovery
   Early Career Researcher Award (DE200101618) , held by MJP. DGH is
   supported by an Australian Commonwealth Government Research Training
   Program Scholarship. NRH is funded by an Alexander von Hum-boldt
   Experienced Researcher Fellowship. RK is supported by a Monash Graduate
   Scholarship and a Monash International Tuition Scholarship. DM is
   supported in part by a University Research Chair, University of Ottawa.
   JEM is supported by a National Health and Medical Research Council
   Career Development Fellowship (APP1143429) . The funders had no role in
   the study design, decision to publish, or preparation of the manuscript.},
Number-of-Cited-References = {33},
Times-Cited = {13},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {8},
Journal-ISO = {J. Clin. Epidemiol.},
Doc-Delivery-Number = {1C8KO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000793362100001},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000499151700002,
Author = {Jetzek, Thorhildur and Avital, Michel and Bjorn-Andersen, Niels},
Title = {The Sustainable Value of Open Government Data},
Journal = {JOURNAL OF THE ASSOCIATION FOR INFORMATION SYSTEMS},
Year = {2019},
Volume = {20},
Number = {6},
Pages = {702-734},
Abstract = {Building on the promise of open data, government agencies support a
   continuously growing number of open data initiatives that are driven
   mainly by expectations of unprecedented value generation from an
   underutilized resource. Although data, in general, have undoubtedly
   become an essential resource for the economy, it has remained largely
   unclear how, or even whether, open data repositories generate any
   significant value. We addressed this void with a study that examines how
   sustainable value is generated from open data. Subsequently, we
   developed a model that explains how open data generate sustainable value
   through two underlying mechanisms. The first, the information sharing
   mechanism, explicates how open data are beneficial to forging
   informational content that creates value for society through increased
   transparency and improved decision-making. The second, the market
   mechanism, explicates how open data are beneficial as a resource in
   products and services offered on the market, as well as how open data
   are used to make processes more efficient or to satisfy previously unmet
   needs. We tested and validated the model using PLS with secondary
   quantitative data from 76 countries. The study provides empirical
   support to the conjecture that openness of data as well as the digital
   governance and digital infrastructure in a country have a positive
   effect on the country's level of sustainable value. Overall, the study
   provides empirical evidence in favor of nurturing open data culture and
   insights about the conditions that support turning it into sustainable
   value for the benefit of citizens, business organizations, and society
   at large.},
Publisher = {ASSOC INFORMATION SYSTEMS},
Address = {GEORGIA STATE UNIV, 35 BROAD STREET, STE 916-917, ATLANTA, GA 30303 USA},
Type = {Article},
Language = {English},
Affiliation = {Jetzek, T (Corresponding Author), Copenhagen Business Sch, Frederiksberg, Denmark.
   Jetzek, Thorhildur, Copenhagen Business Sch, Frederiksberg, Denmark.
   Avital, Michel, Copenhagen Business Sch, Digitalizat, Frederiksberg, Denmark.
   Bjorn-Andersen, Niels, Copenhagen Business Sch, Business IT, Frederiksberg, Denmark.},
DOI = {10.17705/1jais.00549},
ISSN = {1536-9323},
EISSN = {1558-3457},
Keywords = {Open data; Government Data; Sustainable Value; Information Sharing
   Mechanisms; Market Mechanisms},
Keywords-Plus = {PLS-SEM; TECHNOLOGY; BARRIERS; CREATION; CAPTURE; IMPACT},
Research-Areas = {Computer Science; Information Science \& Library Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Information Science \& Library
   Science},
Author-Email = {ruhilda42@gmail.com
   michel@avital.net
   nba@cbs.dk},
Affiliations = {Copenhagen Business School; Copenhagen Business School; Copenhagen
   Business School},
ResearcherID-Numbers = {Jetzek, Thorhildur/AAB-6637-2021
   Jetzek, Thorhildur/AAA-8198-2020
   },
ORCID-Numbers = {Jetzek, Thorhildur/0000-0002-7933-1130
   Avital, Michel/0000-0002-9089-441X},
Number-of-Cited-References = {98},
Times-Cited = {31},
Usage-Count-Last-180-days = {37},
Usage-Count-Since-2013 = {197},
Journal-ISO = {J. Assoc. Inf. Syst.},
Doc-Delivery-Number = {JQ7WU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000499151700002},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000285831700159,
Author = {McCall, Matthew N. and Uppal, Karan and Jaffee, Harris A. and Zilliox,
   Michael J. and Irizarry, Rafael A.},
Title = {The Gene Expression Barcode: leveraging public data repositories to
   begin cataloging the human and murine transcriptomes},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2011},
Volume = {39},
Number = {1},
Pages = {D1011-D1015},
Month = {JAN},
Abstract = {Various databases have harnessed the wealth of publicly available
   microarray data to address biological questions ranging from
   across-tissue differential expression to homologous gene expression.
   Despite their practical value, these databases rely on relative measures
   of expression and are unable to address the most fundamental
   question-which genes are expressed in a given cell type. The Gene
   Expression Barcode is the first database to provide reliable absolute
   measures of expression for most annotated genes for 131 human and 89
   mouse tissue types, including diseased tissue. This is made possible by
   a novel algorithm that leverages information from the GEO and
   ArrayExpress public repositories to build statistical models that permit
   converting data from a single microarray into expressed/unexpressed
   calls for each gene. For selected platforms, users may upload data and
   obtain results in a matter of seconds. The raw data, curated annotation,
   and code used to create our resource are also available at
   http://rafalab.jhsph.edu/barcode.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Irizarry, RA (Corresponding Author), Johns Hopkins Univ, Dept Biostat, Bloomberg Sch Publ Hlth, 615 N Wolfe St, Baltimore, MD 21205 USA.
   McCall, Matthew N.; Jaffee, Harris A.; Irizarry, Rafael A., Johns Hopkins Univ, Dept Biostat, Bloomberg Sch Publ Hlth, Baltimore, MD 21205 USA.
   Zilliox, Michael J., Emory Univ, Sch Med, Dept Microbiol \& Immunol, Atlanta, GA 30322 USA.},
DOI = {10.1093/nar/gkq1259},
ISSN = {0305-1048},
Keywords-Plus = {MOUSE ORTHOLOGOUS GENES; CONSERVATION; PROFILES},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {mzillio@emory.edu
   rafa@jhu.edu},
Affiliations = {Johns Hopkins University; Johns Hopkins Bloomberg School of Public
   Health; Emory University},
ORCID-Numbers = {Uppal, Karan/0000-0001-5985-1668},
Funding-Acknowledgement = {National Institutes of Health {[}GM083084, RR021967, UL1RR025005,
   T32GM074906]; National Cancer Institute {[}CA132480];  {[}R01GM083084]},
Funding-Text = {National Institutes of Health, partial (GM083084, RR021967 and
   UL1RR025005 to R. A. I.); National Cancer Institute (CA132480 to
   M.J.Z.); National Institutes of Health, partial (T32GM074906 to M.N.M.).
   Funding for open access charge: R01GM083084.},
Number-of-Cited-References = {16},
Times-Cited = {137},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {701PA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000285831700159},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000856101300001,
Author = {Samuel, G. and Hardcastle, F. and Broekstra, R. and Lucassen, A.},
Title = {Exploring how biobanks communicate the possibility of commercial access
   and its associated benefits and risks in participant documents},
Journal = {BMC MEDICAL ETHICS},
Year = {2022},
Volume = {23},
Number = {1},
Month = {SEP 21},
Abstract = {Background Biobanks and biomedical research data repositories collect
   their samples and associated data from volunteer participants. Their
   aims are to facilitate biomedical research and improve health, and they
   are framed in terms of contributing to the public good. Biobank
   resources may be accessible to researchers with commercial motivations,
   for example, researchers in pharmaceutical companies who may utilise the
   data to develop new clinical therapeutics and pharmaceutical drugs.
   Studies exploring citizen perceptions of public/private interactions
   associated with large health data repositories/biobanks indicate that
   there are sensitivities around public/private and/or non-profit/profit
   relationships and international sample and data sharing. Less work has
   explored how biobanks communicate their public/private partnerships to
   the public or to their potential research participants. Methods We
   explored how a biobank's aims, benefits and risks, and private/public
   relationships have been framed in public facing recruitment documents
   (consent forms and participant information sheets). Results Biobank
   documents often communicate their commercial access arrangements but not
   the detail about what these interactions would entail, and how risks and
   benefits would be distributed to the public. Conclusion We argue that
   this leads to a polarised discourse between public and private entities
   and/or activities, and fails to attend to the blurred lines between
   them. This results in a lack of attention to more important issues such
   as how risks and benefits in general are distributed to the public. We
   call for a nuanced approach that can contribute to the much-needed
   dialogue in this space.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Samuel, G (Corresponding Author), Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England.
   Samuel, G (Corresponding Author), Univ Oxford, Ctr Personalised Med, Oxford OX3 7BN, England.
   Samuel, G (Corresponding Author), Univ Southampton, Fac Med, Clin Eth Law \& Soc Res Grp, Tremona Rd, Southampton SO16 6YD, Hants, England.
   Samuel, G (Corresponding Author), Univ Southampton, Southampton NIHR Biomed Res Ctr, Tremona Rd, Southampton SO16 6YD, Hants, England.
   Samuel, G.; Hardcastle, F.; Lucassen, A., Univ Oxford, Wellcome Trust Ctr Human Genet, Oxford OX3 7BN, England.
   Samuel, G.; Hardcastle, F.; Lucassen, A., Univ Oxford, Ctr Personalised Med, Oxford OX3 7BN, England.
   Samuel, G.; Broekstra, R.; Lucassen, A., Univ Southampton, Fac Med, Clin Eth Law \& Soc Res Grp, Tremona Rd, Southampton SO16 6YD, Hants, England.
   Samuel, G.; Broekstra, R.; Lucassen, A., Univ Southampton, Southampton NIHR Biomed Res Ctr, Tremona Rd, Southampton SO16 6YD, Hants, England.
   Broekstra, R., Univ Groningen, Univ Med Ctr Groningen Groningen, Dept Hlth Sci, Sect Hlth Psychol, Antonius Deusinglaan 1, NL-9713 AV Groningen, Netherlands.},
DOI = {10.1186/s12910-022-00829-1},
Article-Number = {95},
ISSN = {1472-6939},
Keywords = {Biobanking; health research data repositories; Data access consent;
   Recruitment; Ethics; Public private relationships},
Keywords-Plus = {GENOMIC DATA},
Research-Areas = {Social Sciences - Other Topics; Medical Ethics; Biomedical Social
   Sciences},
Web-of-Science-Categories  = {Ethics; Medical Ethics; Social Sciences, Biomedical},
Author-Email = {gabbysamuel@gmail.com},
Affiliations = {University of Oxford; Wellcome Centre for Human Genetics; University of
   Oxford; University of Southampton; University of Southampton; University
   of Groningen},
ResearcherID-Numbers = {hardcastle, faranak/HKW-7708-2023
   },
ORCID-Numbers = {hardcastle, faranak/0000-0003-4629-9557
   Samuel, Gabby/0000-0001-8111-2730
   Broekstra, Reinder/0000-0002-9269-1245},
Funding-Acknowledgement = {Wellcome {[}219629/Z/19/Z]},
Funding-Text = {This work was supported by the Wellcome under Grant number:
   219629/Z/19/Z. For the purpose of open access, the author will apply a
   CC BY public copyright licence to any Author Accepted Manuscript version
   arising from this submission.},
Number-of-Cited-References = {35},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {BMC Med. Ethics},
Doc-Delivery-Number = {4Q5CV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000856101300001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000644815700007,
Author = {Quinteros, Javier and Carter, Jerry A. and Schaeffer, Jonathan and
   Trabant, Chad and Pedersen, Helle A.},
Title = {Exploring Approaches for Large Data in Seismology: User and Data
   Repository Perspectives},
Journal = {SEISMOLOGICAL RESEARCH LETTERS},
Year = {2021},
Volume = {92},
Number = {3},
Pages = {1531-1540},
Month = {MAY},
Abstract = {New data acquisition techniques are generating data at much finer
   temporal and spatial resolution, compared to traditional seismic
   experiments. This is a challenge for data centers and users. As the
   amount of data potentially flowing into data centers increases by one or
   two orders of magnitude, data management challenges are found throughout
   all stages of the data flow. The Incorporated Research Institutions for
   Seismology?R?seau sismologique et g?od?sique fran?ais and
   GEOForschungsNetz data centers?carried out a survey and conducted
   interviews of users working with very large datasets to understand their
   needs and expectations. One of the conclusions is that existing data
   formats and services are not well suited for users of large datasets.
   Data centers are exploring storage solutions, data formats, and data
   delivery options to meet large dataset user needs. New approaches will
   need to be discussed within the community, to establish large dataset
   standards and best practices, perhaps through participation of
   stakeholders and users in discussion groups and forums.},
Publisher = {SEISMOLOGICAL SOC AMER},
Address = {400 EVELYN AVE, SUITE 201, ALBANY, CA 94706-1375 USA},
Type = {Article},
Language = {English},
Affiliation = {Quinteros, J (Corresponding Author), Potsdam Deutsch GeoForschungsZentrum GFZ, Helmholtz Zentrum, Potsdam, Germany.
   Quinteros, Javier, Potsdam Deutsch GeoForschungsZentrum GFZ, Helmholtz Zentrum, Potsdam, Germany.
   Carter, Jerry A.; Trabant, Chad, Inc Res Inst Seismol IRIS, Seattle, WA USA.
   Schaeffer, Jonathan; Pedersen, Helle A., Univ Grenoble Alpes, OSUG, CNRS, INRAE,IRD,Meteo France, Grenoble, France.
   Pedersen, Helle A., Univ Grenoble Alpes, Univ Savoie Mt Blanc, ISTerre, UGE,IRD,CNRS, F-38000 Grenoble, France.},
DOI = {10.1785/0220200390},
ISSN = {0895-0695},
EISSN = {1938-2057},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {javier@gfz-potsdam.de},
Affiliations = {Helmholtz Association; Helmholtz-Center Potsdam GFZ German Research
   Center for Geosciences; INRAE; Centre National de la Recherche
   Scientifique (CNRS); Communaute Universite Grenoble Alpes; Universite
   Grenoble Alpes (UGA); Institut de Recherche pour le Developpement (IRD);
   Universite Savoie Mont Blanc; Communaute Universite Grenoble Alpes;
   Universite Grenoble Alpes (UGA); Centre National de la Recherche
   Scientifique (CNRS); Institut de Recherche pour le Developpement (IRD);
   Universite Gustave-Eiffel},
ResearcherID-Numbers = {Quinteros, Javier/G-2897-2012
   Pedersen, Helle/AGR-3227-2022
   Pedersen, Helle/E-4927-2017
   },
ORCID-Numbers = {Quinteros, Javier/0000-0001-9993-4003
   Pedersen, Helle/0000-0003-2936-8047
   Pedersen, Helle/0000-0003-2936-8047
   Trabant, Chad/0000-0002-6184-3568},
Funding-Acknowledgement = {European Union {[}821115, 857650]; National Science Foundation (NSF)
   {[}EAR-1851048]; System of Observation and Experimentation for Research
   and the Environment (SOERE); Ministry of Ecological Transition; national
   French funding program Investissements d'Avenir {[}11-EQPX-0040]},
Funding-Text = {The authors thank the users and data providers for their continuous
   feedback, and, in particular, the users who participated in the survey.
   Javier Quinteros collaborated in this work as a part of the European
   Open Science Cloud (EOSC)-Pillar project, which has received funding
   from the European Union's Horizon 2020 research and innovation program
   under Grant Agreement Number 857650, as well as the Real-time earthquake
   rIsk reduction for a reSilient Europe (RISE) project, also supported by
   the European Union's Horizon 2020 research and innovation program under
   Grant Agreement Number 821115. GEOForschungsNetz (GEOFON) operates the
   GeoForschungsZentrum (GFZ) seismological data archive, where own and
   third party data are curated alongside with data from passive
   Geophysical Instrument Pool Potsdam (GIPP) experiments. The
   seismological facility for the advancement of geoscience (SAGE) is
   operated by Incorporated Research Institutions for Seismology (IRIS) on
   behalf of the National Science Foundation (NSF) through Award
   EAR-1851048. The Reseau sismologique et geodesique francais (RESIF) data
   center is operated on behalf of the RESIF consortium, a national
   research infrastructure coordinated by Centre National de la Recherche
   Scientifique (CNRS) and which receives funding, personnel and other from
   all the consortium members. Resif-SI is also supported by the System of
   Observation and Experimentation for Research and the Environment (SOERE)
   and by the Ministry of Ecological Transition. Resif-SI has benefited
   from the Resif-CORE project (11-EQPX-0040), funded by the national
   French funding program Investissements d'Avenir and managed by the
   French National Research Agency (ANR).},
Number-of-Cited-References = {13},
Times-Cited = {10},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Seismol. Res. Lett.},
Doc-Delivery-Number = {RU0AW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000644815700007},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000445614800026,
Author = {Maranville, Brian and Ratcliff, II, William and Kienzle, Paul},
Title = {<i>reductus</i>: a stateless Python data reduction service with a
   browser front end},
Journal = {JOURNAL OF APPLIED CRYSTALLOGRAPHY},
Year = {2018},
Volume = {51},
Number = {5},
Pages = {1500-1506},
Month = {OCT},
Abstract = {The online data reduction service reductus transforms measurements in
   experimental science from laboratory coordinates into physically
   meaningful quantities with accurate estimation of uncertainties from
   instrumental settings and properties. This reduction process is based on
   a few well known transformations, but flexibility in the application of
   the transforms and algorithms supports flexibility in experiment design,
   enabling a broader range of measurements than a rigid reduction scheme
   for data. The user interface allows easy construction of arbitrary
   pipelines from well known data transforms using a visual data flow
   diagram. Source data are drawn from a networked, open data repository.
   The Python back end uses intelligent caching to store intermediate
   results of calculations for a highly responsive user experience. The
   reference implementation allows immediate reduction of measurements as
   they are recorded for the three neutron reflectometry instruments at the
   NIST Center for Neutron Research, without the need for visiting
   scientists to install additional software on their own computers.},
Publisher = {INT UNION CRYSTALLOGRAPHY},
Address = {2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Maranville, B (Corresponding Author), NIST Ctr Neutron Res, 100 Bur Dr, Gaithersburg, MD 20899 USA.
   Maranville, Brian; Ratcliff, William, II; Kienzle, Paul, NIST Ctr Neutron Res, 100 Bur Dr, Gaithersburg, MD 20899 USA.},
DOI = {10.1107/S1600576718011974},
ISSN = {1600-5767},
Keywords = {neutron reflectometry; X-ray reflectometry; data reduction; computer
   programs},
Research-Areas = {Chemistry; Crystallography},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary; Crystallography},
Author-Email = {brian.maranville@nist.gov},
Affiliations = {National Institute of Standards \& Technology (NIST) - USA},
ResearcherID-Numbers = {Maranville, Brian/T-1497-2017
   },
ORCID-Numbers = {Maranville, Brian/0000-0002-6105-8789
   Kienzle, Paul/0000-0002-7893-0318
   Ratcliff, William/0000-0001-8956-3851},
Funding-Acknowledgement = {NSF CHRNS {[}DMR-1508249]},
Funding-Text = {Significant contributions to the early code were made by Brendan Rowan,
   Alex Yee, Ophir Lifshitz and Elakian Kanakaraj as part of the NIST
   Summer High School Internship Program (SHIP) and Joseph Redmon as part
   of the Summer Undergraduate Research Fellowship (SURF), supported by NSF
   CHRNS grant DMR-1508249.},
Number-of-Cited-References = {10},
Times-Cited = {41},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {J. Appl. Crystallogr.},
Doc-Delivery-Number = {GU8TI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000445614800026},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000466551600139,
Author = {Altuzarra, Amaia and Galvez-Galvez, Catalina and Gonzalez-Flores, Ana},
Title = {Economic Development and Female Labour Force Participation: The Case of
   European Union Countries},
Journal = {SUSTAINABILITY},
Year = {2019},
Volume = {11},
Number = {7},
Month = {APR 1},
Abstract = {In this paper, we studied the relationship between female labour force
   participation and economic development in the 28 countries of the
   European Union during the period 1990-2016. The analysis was carried out
   from two different viewpoints: first, we studied all the countries of
   the EU-28, and second, the evidence was disaggregated into two groups of
   countries: old (EU-15) and new (EU-13) member estates. The data used
   came from the World Bank open data repository and Eurostat. The
   methodology used consisted of the estimation of static (Ordinary Least
   Squares (OLS) and Fixed Effects (FE)) and dynamic (generalized moments
   modelGMM) models. Results for all European countries (EU-28) were
   consistent with the hypothesis which suggests the existence of a
   U-shaped relationship between female labour force participation and
   economic development. When the sample was broken down into groups, we
   found evidence that confirms the feminization hypothesis for the new
   countries of the EU, but not for the old ones.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Galvez-Galvez, C (Corresponding Author), Univ Basque Country, UPV EHU, Fac Econ \& Business, Av Lehendakari Agirre 83, Bilbao 48015, Spain.
   Altuzarra, Amaia; Galvez-Galvez, Catalina; Gonzalez-Flores, Ana, Univ Basque Country, UPV EHU, Fac Econ \& Business, Av Lehendakari Agirre 83, Bilbao 48015, Spain.},
DOI = {10.3390/su11071962},
Article-Number = {1962},
EISSN = {2071-1050},
Keywords = {regional economic development; female labour force; education; static
   and dynamic models; O10; O52; J21},
Keywords-Plus = {FEMINIZATION; GROWTH; WOMEN},
Research-Areas = {Science \& Technology - Other Topics; Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Green \& Sustainable Science \& Technology; Environmental Sciences;
   Environmental Studies},
Author-Email = {amaia.altuzarra@ehu.eus
   catalina.galvez@ehu.eus
   ana.gonzalezflores@ehu.eus},
Affiliations = {University of Basque Country},
ResearcherID-Numbers = {Altuzarra, Amaia/A-4476-2019
   GALVEZ, CATALINA GALVEZ/Y-5532-2019
   Flores, Ana González/Y-2300-2019
   },
ORCID-Numbers = {Altuzarra, Amaia/0000-0002-9256-0050
   Flores, Ana González/0000-0002-8228-5868
   GALVEZ GALVEZ, CATALINA/0000-0001-7398-8599},
Funding-Acknowledgement = {Eusko Jaurlaritza {[}IT1052-16]},
Funding-Text = {This research was funded by Eusko Jaurlaritza, grant number IT1052-16.},
Number-of-Cited-References = {48},
Times-Cited = {18},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Sustainability},
Doc-Delivery-Number = {HW2WV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000466551600139},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001048362100001,
Author = {Bogue, Molly A. and Ball, Robyn L. and Walton, David O. and Dunn,
   Matthew H. and Kolishovski, Georgi and Berger, Alexander and Lamoureux,
   Anna and Grubb, Stephen C. and Gerring, Matthew and Kim, Matthew and
   Liang, Hongping and Emerson, Jake and Stearns, Timothy and He, Hao and
   Mukherjee, Gaurab and Bluis, John and Davis, Sara and Desai, Sejal and
   Sundberg, Beth and Kadakkuzha, Beena and Kunde-Ramamoorthy, Govindarajan
   and Philip, Vivek M. and Chesler, Elissa J.},
Title = {Mouse phenome database: curated data repository with interactive
   multi-population and multi-trait analyses},
Journal = {MAMMALIAN GENOME},
Year = {2023},
Volume = {34},
Number = {4},
Pages = {509-519},
Month = {DEC},
Abstract = {The Mouse Phenome Database continues to serve as a curated repository
   and analysis suite for measured attributes of members of diverse mouse
   populations. The repository includes annotation to community standard
   ontologies and guidelines, a database of allelic states for 657 mouse
   strains, a collection of protocols, and analysis tools for flexible,
   interactive, user directed analyses that increasingly integrates data
   across traits and populations. The database has grown from its initial
   focus on a standard set of inbred strains to include heterogeneous mouse
   populations such as the Diversity Outbred and mapping crosses and well
   as Collaborative Cross, Hybrid Mouse Diversity Panel, and recombinant
   inbred strains. Most recently the system has expanded to include data
   from the International Mouse Phenotyping Consortium. Collectively these
   data are accessible by API and provided with an interactive tool suite
   that enables users' persistent selection, storage, and operation on
   collections of measures. The tool suite allows basic analyses, advanced
   functions with dynamic visualization including multi-population
   meta-analysis, multivariate outlier detection, trait pattern matching,
   correlation analyses and other functions. The data resources and
   analysis suite provide users a flexible environment in which to explore
   the basis of phenotypic variation in health and disease across the
   lifespan.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Bogue, MA (Corresponding Author), Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA.
   Bogue, Molly A.; Ball, Robyn L.; Walton, David O.; Dunn, Matthew H.; Kolishovski, Georgi; Berger, Alexander; Lamoureux, Anna; Grubb, Stephen C.; Gerring, Matthew; Liang, Hongping; Emerson, Jake; Stearns, Timothy; He, Hao; Mukherjee, Gaurab; Bluis, John; Davis, Sara; Desai, Sejal; Sundberg, Beth; Kadakkuzha, Beena; Kunde-Ramamoorthy, Govindarajan; Philip, Vivek M.; Chesler, Elissa J., Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA.
   Kim, Matthew, Univ British Columbia, Vancouver, BC, Canada.},
DOI = {10.1007/s00335-023-10014-3},
EarlyAccessDate = {AUG 2023},
ISSN = {0938-8990},
EISSN = {1432-1777},
Keywords-Plus = {GENOME; REPRODUCIBILITY},
Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
   Microbiology; Genetics \& Heredity},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
   Microbiology; Genetics \& Heredity},
Author-Email = {Molly.Bogue@jax.org},
Affiliations = {Jackson Laboratory; University of British Columbia},
Funding-Acknowledgement = {National Institutes of Health {[}DA028420, AG066346, DA039841,
   OD030187]; JAX Cancer Center Support Grant {[}P30 CA03419]; Jackson
   Laboratory Director's Innovation Fund; Jackson Laboratory Cube
   Initiative; National Institutes of Health; NIDA},
Funding-Text = {This work was supported by the National Institutes of Health
   {[}DA028420, AG066346 to MAB; DA039841, OD030187 to EJC and RLB]. We
   gratefully acknowledge the contribution of members of the Computational
   Sciences Service at The Jackson Laboratory supported by the JAX Cancer
   Center Support Grant (P30 CA034196) for expert assistance with the work
   described in this publication. Additional support came from The Jackson
   Laboratory Director's Innovation Fund and The Jackson Laboratory Cube
   Initiative. Funding for open access charge: National Institutes of
   Health, NIDA.},
Number-of-Cited-References = {35},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Mamm. Genome},
Doc-Delivery-Number = {W6HD4},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001048362100001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000485307400003,
Author = {Zhang, Ruojing and Indulska, Marta and Sadiq, Shazia},
Title = {Discovering Data Quality Problems The Case of Repurposed Data},
Journal = {BUSINESS \& INFORMATION SYSTEMS ENGINEERING},
Year = {2019},
Volume = {61},
Number = {5},
Pages = {575-593},
Month = {OCT},
Abstract = {Existing methodologies for identifying data quality problems are
   typically user-centric, where data quality requirements are first
   determined in a top-down manner following well-established design
   guidelines, organizational structures and data governance frameworks. In
   the current data landscape, however, users are often confronted with
   new, unexplored datasets that they may not have any ownership of, but
   that are perceived to have relevance and potential to create value for
   them. Such repurposed datasets can be found in government open data
   portals, data markets and several publicly available data repositories.
   In such scenarios, applying top-down data quality checking approaches is
   not feasible, as the consumers of the data have no control over its
   creation and governance. Hence, data consumers - data scientists and
   analysts - need to be empowered with data exploration capabilities that
   allow them to investigate and understand the quality of such datasets to
   facilitate well-informed decisions on their use. This research aims to
   develop such an approach for discovering data quality problems using
   generic exploratory methods that can be effectively applied in settings
   where data creation and use is separated. The approach, named LANG, is
   developed through a Design Science approach on the basis of semiotics
   theory and data quality dimensions. LANG is empirically validated in
   terms of soundness of the approach, its repeatability and
   generalizability.},
Publisher = {SPRINGER VIEWEG-SPRINGER FACHMEDIEN WIESBADEN GMBH},
Address = {ABRAHAM-LINCOLN STASSE 46, WIESBADEN, 65189, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Indulska, M (Corresponding Author), Univ Queensland, Business Sch, St Lucia, Qld 4072, Australia.
   Zhang, Ruojing; Sadiq, Shazia, Univ Queensland, Sch Informat Technol \& Elect Engn, St Lucia, Qld 4072, Australia.
   Indulska, Marta, Univ Queensland, Business Sch, St Lucia, Qld 4072, Australia.},
DOI = {10.1007/s12599-019-00608-0},
ISSN = {2363-7005},
EISSN = {1867-0202},
Keywords = {Data quality; Open data; Design science},
Keywords-Plus = {DESIGN SCIENCE RESEARCH; BIG DATA; INFORMATION; SYSTEMS; METHODOLOGY;
   FRAMEWORK},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Author-Email = {r.zhang3@uq.edu.au
   m.indulska@business.uq.edu.au
   shazia@itee.uq.edu.au},
Affiliations = {University of Queensland; University of Queensland},
ResearcherID-Numbers = {Indulska, Marta/A-7170-2009
   Sadiq, Shazia/C-8593-2016},
ORCID-Numbers = {Indulska, Marta/0000-0002-2156-4097
   Sadiq, Shazia/0000-0001-6739-4145},
Number-of-Cited-References = {81},
Times-Cited = {14},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {68},
Journal-ISO = {Bus. Inf. Syst. Eng.},
Doc-Delivery-Number = {IW9IQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000485307400003},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000809645500001,
Author = {Hutt, Stephen and Baker, Ryan S. and Ashenafi, Michael Mogessie and
   Andres-Bray, Juan Miguel and Brooks, Christopher},
Title = {Controlled outputs, full data: A privacy-protecting infrastructure for
   MOOC data},
Journal = {BRITISH JOURNAL OF EDUCATIONAL TECHNOLOGY},
Year = {2022},
Volume = {53},
Number = {4},
Pages = {756-775},
Month = {JUL},
Abstract = {Learning analytics research presents challenges for researchers
   embracing the principles of open science. Protecting student privacy is
   paramount, but progress in increasing scientific understanding and
   improving educational outcomes depends upon open, scalable and
   replicable research. Findings have repeatedly been shown to be
   contextually dependent on personal and demographic variables, so how can
   we use this data in a manner that is ethical and secure for all
   involved? This paper presents ongoing work on the MOOC Replication
   Framework (MORF), a big data repository and analysis environment for
   Massive Open Online Courses (MOOCs). We discuss MORF's approach to
   protecting student privacy, which allows researchers to use data without
   having direct access. Through an open API, documentation and tightly
   controlled outputs, this framework provides researchers with the
   opportunity to perform secure, scalable research and facilitates
   collaboration, replication, and novel research. We also highlight ways
   in which MORF represents a solution template to issues surrounding
   privacy and security in the age of big data in education and key
   challenges still to be tackled.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Hutt, S; Baker, RS (Corresponding Author), Univ Penn, 3700 Walnut St, Philadelphia, PA 19104 USA.
   Hutt, Stephen; Baker, Ryan S.; Andres-Bray, Juan Miguel, Univ Penn, Grad Sch Educ, Philadelphia, PA 19104 USA.
   Ashenafi, Michael Mogessie, Carnegie Mellon Univ, Human Comp Interact Inst, Pittsburgh, PA USA.
   Brooks, Christopher, Univ Michigan, Sch Informat, Ann Arbor, MI USA.},
DOI = {10.1111/bjet.13231},
EarlyAccessDate = {MAY 2022},
ISSN = {0007-1013},
EISSN = {1467-8535},
Keywords = {data repository; data sharing; MOOC data; MOOC Replication Framework
   (MORF); open educational science; personal identifying information;
   privacy-protecting infrastructure},
Research-Areas = {Education \& Educational Research},
Web-of-Science-Categories  = {Education \& Educational Research},
Author-Email = {hutts@upenn.edu
   rybaker@upenn.edu},
Affiliations = {University of Pennsylvania; Carnegie Mellon University; University of
   Michigan System; University of Michigan},
ResearcherID-Numbers = {Baker, Ryan/IWE-2102-2023
   },
ORCID-Numbers = {Hutt, Stephen/0000-0002-7041-7472
   Andres-Bray, Miggy/0000-0001-7126-7819
   Brooks, Christopher/0000-0003-0875-0204},
Funding-Acknowledgement = {National Science Foundation; University of Pennsylvania},
Funding-Text = {National Science Foundation; University of Pennsylvania},
Number-of-Cited-References = {53},
Times-Cited = {4},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {17},
Journal-ISO = {Br. J. Educ. Technol.},
Doc-Delivery-Number = {8E5IS},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000809645500001},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000407347300017,
Author = {Wandelt, Sebastian and Wang, Zezhou and Sun, Xiaoqian},
Title = {Worldwide Railway Skeleton Network: Extraction Methodology and
   Preliminary Analysis},
Journal = {IEEE TRANSACTIONS ON INTELLIGENT TRANSPORTATION SYSTEMS},
Year = {2017},
Volume = {18},
Number = {8},
Pages = {2206-2216},
Month = {AUG},
Abstract = {Understanding and improving global mobility has gained increased
   interest during the last decades. However, studies on the railway
   network are spatially limited so far, mostly investigating the domestic
   network of a country. Data availability is a major limiting factor for
   the analysis of these networks. Despite the increased open data
   movement, network operators are often reluctant to publish their
   infrastructure and passenger data. Existing large-scale studies usually
   make use of hand-collected data, for instance, based on historical
   cartographies. In this paper, we develop and implement a methodology to
   extract the worldwide railway skeleton network from the open data
   repository OpenStreetMap, where nodes are stations/waypoints and links
   are weights with information such as spatial distance, gauge, and
   maximum speed. We describe how we solved several data cleansing and
   scalability issues and developed network simplification techniques, in
   order to obtain an adequate representation of the network. We show that
   the network breaks down into few large and many small components.
   Furthermore, we show that this public data set can be used for efficient
   minimum travel time estimation between stations or cities. This paper
   leads to the development of a new research data set and contributes
   toward the ability of analyzing global mobility patterns, particularly
   regarding multimodality and cross-country transportation.},
Publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC},
Address = {445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA},
Type = {Article},
Language = {English},
Affiliation = {Sun, XQ (Corresponding Author), Beihang Univ, Sch Elect \& Informat Engn, Beijing 100191, Peoples R China.
   Wandelt, Sebastian; Wang, Zezhou; Sun, Xiaoqian, Beihang Univ, Sch Elect \& Informat Engn, Beijing 100191, Peoples R China.
   Wandelt, Sebastian; Sun, Xiaoqian, Beijing Key Lab Network Based Cooperat ATM, Beijing 100191, Peoples R China.},
DOI = {10.1109/TITS.2016.2632998},
ISSN = {1524-9050},
EISSN = {1558-0016},
Keywords = {Worldwide railway network; OpenStreetMap; global mobility},
Keywords-Plus = {HIGH-SPEED RAIL; AIR TRANSPORT; COMPLEX NETWORKS; INTEGRATION;
   COMPETITION; SEARCH; MODELS; CHINA},
Research-Areas = {Engineering; Transportation},
Web-of-Science-Categories  = {Engineering, Civil; Engineering, Electrical \& Electronic;
   Transportation Science \& Technology},
Author-Email = {wandelt@informatik.hu-berlin.de
   wangzezai@buaa.edu.cn
   sunxq@buaa.edu.cn},
Affiliations = {Beihang University},
ResearcherID-Numbers = {Wandelt, Sebastian/ISB-7340-2023
   Wang, Zezhou/V-4424-2019},
ORCID-Numbers = {Wang, Zezhou/0000-0003-4292-7341},
Funding-Acknowledgement = {National Natural Science Foundation of China {[}61650110516, 61601013];
   Research Fund for International Young Scientists},
Funding-Text = {This work was supported in part by the Research Fund for International
   Young Scientists, in part by the National Natural Science Foundation of
   China under Grant 61650110516, in part by the Research Fund for Young
   Scientists, and in part by the National Natural Science Foundation of
   China under Grant 61601013. The Associate Editor for this paper was P.
   Ioannou.},
Number-of-Cited-References = {36},
Times-Cited = {15},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {27},
Journal-ISO = {IEEE Trans. Intell. Transp. Syst.},
Doc-Delivery-Number = {FD2ED},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000407347300017},
DA = {2024-01-15},
}

@article{ WOS:000692679900053,
Author = {Forsstrom, Petri R. and Juola, Jussi and Rautiainen, Miina},
Title = {Relationships between understory spectra and fractional cover in
   northern European boreal forests},
Journal = {AGRICULTURAL AND FOREST METEOROLOGY},
Year = {2021},
Volume = {308},
Month = {OCT 15},
Abstract = {Modern satellite and airborne optical images have increasingly higher
   resolutions and enable the study of all layers of forests, not just the
   forest canopy. To understand the contribution of different types of
   understory on the overall spectral reflectance signal, ground reference
   data are needed from different types of forests. In this paper, we
   present the analysis of spectral reflectance factors (350-2300 nm) and
   fractional covers of understory from 36 boreal forest stands. The data
   were collected during peak growing season in a southern boreal forest
   area in Finland. The study stands represent four different forest site
   fertility types. We used a spectrometer to measure understory spectra in
   nadir and vegetation quadrats to estimate fractional cover. We showed
   that the understory has specific spectral features related to the site
   fertility type and fractional cover. Our results suggest that remote
   sensing can be used to differentiate forest site fertility types and
   estimate understory green fractional cover in northern European boreal
   forests. The collected data are openly available in an open data
   repository.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Forsström, PR (Corresponding Author), Aalto Univ, Dept Built Environm, POB 14100, Aalto 00076, Finland.
   Forsstrom, Petri R.; Juola, Jussi; Rautiainen, Miina, Aalto Univ, Dept Built Environm, POB 14100, Aalto 00076, Finland.
   Rautiainen, Miina, Aalto Univ, Dept Elect \& Nanoengn, POB 15500, Aalto 00076, Finland.},
DOI = {10.1016/j.agrformet.2021.108604},
EarlyAccessDate = {AUG 2021},
Article-Number = {108604},
ISSN = {0168-1923},
EISSN = {1873-2240},
Keywords = {Forest reflectance; Forest site type; Vegetation index; Hyperspectral},
Keywords-Plus = {SEASONAL DYNAMICS; BRDF DATA; REFLECTANCE; VEGETATION; RETRIEVAL; NDVI},
Research-Areas = {Agriculture; Forestry; Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Agronomy; Forestry; Meteorology \& Atmospheric Sciences},
Author-Email = {petri.forsstrom@aalto.fi
   jussi.juola@aalto.fi
   miina.a.rautiainen@aalto.fi},
Affiliations = {Aalto University; Aalto University},
ResearcherID-Numbers = {Rautiainen, Miina/A-4208-2009
   },
ORCID-Numbers = {Rautiainen, Miina/0000-0002-6568-3258
   Forsstrom, Petri/0000-0002-2357-2517
   Juola, Jussi/0000-0002-6050-7247},
Funding-Acknowledgement = {Academy of Finland {[}286390, 3323004]; European Research Council (ERC)
   under the European Union's Horizon 2020 research and innovation
   programme {[}771049]; Academy of Finland (AKA) {[}286390] Funding
   Source: Academy of Finland (AKA)},
Funding-Text = {We thank Aarne Hovi, Ville Ranta, and Daniel Schraik for collaboration.
   This work was supported by the Academy of Finland {[}BOREALITY, grant
   number 286390; and DIMEBO, grant number 3323004]; and by the European
   Research Council (ERC) under the European Union's Horizon 2020 research
   and innovation programme {[}grant agreement No 771049]. The article
   reflects only the authors' view and the Agency is not responsible for
   any use that may be made of the information it contains.},
Number-of-Cited-References = {36},
Times-Cited = {6},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Agric. For. Meteorol.},
Doc-Delivery-Number = {UL5GS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000692679900053},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000538172000004,
Author = {Avila Barrientos, Eder},
Title = {ANALYSIS OF THE PRINCIPLES FOR THE DESCRIPTION OF RESEARCH DATA BY
   DATACITE METADATA SCHEMA},
Journal = {ANALES DE DOCUMENTACION},
Year = {2020},
Volume = {23},
Number = {1},
Abstract = {The objective of this work is to analyze the theoretical-methodological
   principles related to the description of the research data. An analysis
   was carried out on the status of the research data issue, which
   addresses aspects of its citation, description and systematization.
   Metadata elements for the description of research data sets that are
   included in the Metadata Schema DataCite were identified and analyzed,
   with the purpose of creating a proposed descriptive profile applicable
   to these sets. It is estimated that, if the research data is properly
   described, then its accessibility and reuse will be further promoted. To
   do this, it is necessary for academic and research institutions to
   participate in the generation of open access policies for their research
   data.},
Publisher = {EDIT UM-EDICIONES UNIV MURCIA},
Address = {EDIFICIO SAAVEDRA FAJARDO, C/O ACTOR ISIDORO MAIQUEZ 9, MURCIA, 30007,
   SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {Barrientos, EA (Corresponding Author), Univ Nacl Autonoma Mexico, Inst Invest Bibliotecol \& Informac, Mexico City, DF, Mexico.
   Avila Barrientos, Eder, Univ Nacl Autonoma Mexico, Inst Invest Bibliotecol \& Informac, Mexico City, DF, Mexico.},
DOI = {10.6018/analesdoc.400341},
ISSN = {1575-2437},
EISSN = {1697-7904},
Keywords = {research data; description; retrieval; data repository},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {eder@iibi.unam.mx},
Affiliations = {Universidad Nacional Autonoma de Mexico},
ResearcherID-Numbers = {Ávila, Eder/GLR-5889-2022},
Number-of-Cited-References = {22},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {An. Doc.},
Doc-Delivery-Number = {LV0ZK},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000538172000004},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:001012054900001,
Author = {Borycz, Joshua and Olendorf, Robert and Specht, Alison and Grant, Bruce
   and Crowston, Kevin and Tenopir, Carol and Allard, Suzie and Rice,
   Natalie M. and Hu, Rachael and Sandusky, Robert J.},
Title = {Perceived benefits of open data are improving but scientists still lack
   resources, skills, and rewards},
Journal = {HUMANITIES \& SOCIAL SCIENCES COMMUNICATIONS},
Year = {2023},
Volume = {10},
Number = {1},
Month = {JUN 20},
Abstract = {Addressing global scientific challenges requires the widespread sharing
   of consistent and trustworthy research data. Identifying the factors
   that influence widespread data sharing will help us understand the
   limitations and potential leverage points. We used two well-known
   theoretical frameworks, the Theory of Planned Behavior and the
   Technology Acceptance Model, to analyze three DataONE surveys published
   in 2011, 2015, and 2020. These surveys aimed to identify individual,
   social, and organizational influences on data-sharing behavior. In this
   paper, we report on the application of multiple factor analysis (MFA) on
   this combined, longitudinal, survey data to determine how these
   attitudes may have changed over time. The first two dimensions of the
   MFA were named willingness to share and satisfaction with resources
   based on the contributing questions and answers. Our results indicated
   that both dimensions are strongly influenced by individual factors such
   as perceived benefit, risk, and effort. Satisfaction with resources was
   significantly influenced by social and organizational factors such as
   the availability of training and data repositories. Researchers that
   improved in willingness to share are shown to be operating in domains
   with a high reliance on shared resources, are reliant on funding from
   national or federal sources, work in sectors where internal practices
   are mandated, and live in regions with highly effective communication
   networks. Significantly, satisfaction with resources was inversely
   correlated with willingness to share across all regions. We posit that
   this relationship results from researchers learning what resources they
   actually need only after engaging with the tools and procedures
   extensively.},
Publisher = {SPRINGERNATURE},
Address = {CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Borycz, J (Corresponding Author), Vanderbilt Univ, Nashville, TN 37235 USA.
   Borycz, Joshua, Vanderbilt Univ, Nashville, TN 37235 USA.
   Olendorf, Robert, North Carolina State Univ, Raleigh, NC USA.
   Specht, Alison, Univ Queensland, TERN, Brisbane, Australia.
   Grant, Bruce, Widener Univ, Chester, PA USA.
   Crowston, Kevin, Syracuse Univ, Syracuse, NY USA.
   Tenopir, Carol; Allard, Suzie; Rice, Natalie M., Univ Tennessee, Knoxville, TN USA.
   Hu, Rachael, Calif Digital Lib, Oakland, CA USA.
   Sandusky, Robert J., Univ Illinois, Chicago, IL USA.},
DOI = {10.1057/s41599-023-01831-7},
Article-Number = {339},
EISSN = {2662-9992},
Keywords-Plus = {DATA REUSE BEHAVIORS; RESEARCH COLLABORATION; USER ACCEPTANCE; SCIENCE;
   REPRODUCIBILITY; RESEARCHERS; INNOVATION; ATTITUDES; ROLES; NORMS},
Research-Areas = {Arts \& Humanities - Other Topics; Social Sciences - Other Topics},
Web-of-Science-Categories  = {Humanities, Multidisciplinary; Social Sciences, Interdisciplinary},
Author-Email = {joshua.borycz@vanderbilt.edu},
Affiliations = {Vanderbilt University; North Carolina State University; University of
   Queensland; Widener University; Syracuse University; University of
   Tennessee System; University of Tennessee Knoxville; University of
   Illinois System; University of Illinois Chicago; University of Illinois
   Chicago Hospital},
ResearcherID-Numbers = {Crowston, Kevin/C-6068-2008
   },
ORCID-Numbers = {Crowston, Kevin/0000-0003-1996-3600
   Borycz, Joshua/0000-0002-1505-148X
   Specht, Alison/0000-0002-2623-0854
   Olendorf, Robert/0000-0003-3353-5637
   Tenopir, Carol/0000-0002-9056-8251
   Allard, Suzie/0000-0001-9421-3848},
Number-of-Cited-References = {60},
Times-Cited = {0},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Hum. Soc. Sci. Commun.},
Doc-Delivery-Number = {J8KK1},
Web-of-Science-Index = {Social Science Citation Index (SSCI); Arts &amp; Humanities Citation Index (A&amp;HCI)},
Unique-ID = {WOS:001012054900001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000992407100001,
Author = {Pfaff, Emily R. and Girvin, Andrew T. and Crosskey, Miles and
   Gangireddy, Srushti and Master, Hiral and Wei, Wei-Qi and Kerchberger,
   V. Eric and Weiner, Mark and Harris, Paul A. and Basford, Melissa and
   Lunt, Chris and Chute, Christopher G. and Moffitt, Richard A. and
   Haendel, Melissa and N3C RECOVER Consortia},
Title = {De-black-boxing health AI: demonstrating reproducible machine learning
   computable phenotypes using the N3C-RECOVER Long COVID model in the All
   of Us data repository},
Journal = {JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION},
Year = {2023},
Volume = {30},
Number = {7},
Pages = {1305-1312},
Month = {JUN 20},
Abstract = {Machine learning (ML)-driven computable phenotypes are among the most
   challenging to share and reproduce. Despite this difficulty, the urgent
   public health considerations around Long COVID make it especially
   important to ensure the rigor and reproducibility of Long COVID
   phenotyping algorithms such that they can be made available to a broad
   audience of researchers. As part of the NIH Researching COVID to Enhance
   Recovery (RECOVER) Initiative, researchers with the National COVID
   Cohort Collaborative (N3C) devised and trained an ML-based phenotype to
   identify patients highly probable to have Long COVID. Supported by
   RECOVER, N3C and NIH's All of Us study partnered to reproduce the output
   of N3C's trained model in the All of Us data enclave, demonstrating
   model extensibility in multiple environments. This case study in
   ML-based phenotype reuse illustrates how open-source software best
   practices and cross-site collaboration can de-black-box phenotyping
   algorithms, prevent unnecessary rework, and promote open science in
   informatics.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Pfaff, ER (Corresponding Author), Univ North Carolina Chapel Hill, Sch Med, Dept Med, 160 N Med Dr, Chapel Hill, NC 27599 USA.
   Pfaff, Emily R., Univ North Carolina Chapel Hill, Sch Med, Dept Med, 160 N Med Dr, Chapel Hill, NC 27599 USA.
   Girvin, Andrew T., Palantir Technol, Denver, CO USA.
   Crosskey, Miles, CoVar Appl Technol, Durham, NC USA.
   Gangireddy, Srushti; Wei, Wei-Qi; Harris, Paul A., Vanderbilt Univ, Med Ctr, Dept Biomed Informat, Nashville, TN USA.
   Master, Hiral; Basford, Melissa, Vanderbilt Univ, Vanderbilt Inst Clin \& Translat Res, Med Ctr, Nashville, TN USA.
   Kerchberger, V. Eric, Vanderbilt Univ, Med Ctr, Dept Med, Div Allergy Pulm \& Crit Care Med, Nashville, TN USA.
   Weiner, Mark, Weill Cornell Med, Dept Med, New York, NY USA.
   Lunt, Chris, NIH, Bethesda, MD USA.
   Chute, Christopher G., Johns Hopkins Sch Med, Baltimore, MD USA.
   Chute, Christopher G., Johns Hopkins Sch Publ Hlth, Baltimore, MD USA.
   Chute, Christopher G., Johns Hopkins Sch Nursing, Baltimore, MD USA.
   Moffitt, Richard A., Emory Univ, Dept Hematol \& Med Oncol, Atlanta, GA USA.
   Moffitt, Richard A., Emory Univ, Dept Biomed Informat, Atlanta, GA USA.
   Haendel, Melissa, Univ Colorado, Dept Biomed Informat, Anschutz Med Campus, Denver, CO USA.},
DOI = {10.1093/jamia/ocad077},
EarlyAccessDate = {MAY 2023},
ISSN = {1067-5027},
EISSN = {1527-974X},
Keywords = {electronic health records; machine learning; phenotype; SARS-CoV-2},
Research-Areas = {Computer Science; Health Care Sciences \& Services; Information Science
   \& Library Science; Medical Informatics},
Web-of-Science-Categories  = {Computer Science, Information Systems; Computer Science,
   Interdisciplinary Applications; Health Care Sciences \& Services;
   Information Science \& Library Science; Medical Informatics},
Author-Email = {epfaff@email.unc.edu},
Affiliations = {University of North Carolina School of Medicine; University of North
   Carolina; University of North Carolina Chapel Hill; Palantir
   Technologies; Vanderbilt University; Vanderbilt University; Vanderbilt
   University; Cornell University; Weill Cornell Medicine; National
   Institutes of Health (NIH) - USA; Johns Hopkins University; Johns
   Hopkins Medicine; Johns Hopkins University; Johns Hopkins Bloomberg
   School of Public Health; Johns Hopkins University; Emory University;
   Emory University; University of Colorado System; University of Colorado
   Denver; University of Colorado Anschutz Medical Campus},
ResearcherID-Numbers = {Kerchberger, Vern/AAH-2302-2020
   },
ORCID-Numbers = {Kerchberger, Vern/0000-0002-0342-1965
   Master, Hiral/0000-0003-0019-3087
   Pfaff, Emily/0000-0002-6840-9756},
Funding-Acknowledgement = {National Institutes of Health (NIH) {[}3 OT2 OD025315]; CD2H- The
   National COVID Cohort Collaborative (N3C) {[}1 OT2 OD025337]; Office of
   the Director: Regional Medical Centers {[}1 OT2 OD025276]; IAA;
   Federally Qualified Health Centers; Data and Research Center; Biobank;
   Participant Center; Participant Technology Systems Center;
   Communications and Engagement; Community Partners;  {[}OTA OT2HL161847];
   {[}U24TR002306];  {[}1 OT2 OD026549];  {[}1 OT2 OD026554];  {[}1 OT2
   OD026557];  {[}1 OT2 OD026556];  {[}1 OT2 OD026550];  {[}1 OT2 OD
   026552];  {[}1 OT2 OD026553];  {[}1 OT2 OD026548];  {[}1 OT2 OD026551]; 
   {[}1 OT2 OD026555];  {[}AOD21037];  {[}AOD22003];  {[}AOD16037]; 
   {[}AOD21041];  {[}HHSN 263201600085U];  {[}5 U2C OD023196];  {[}1 U24
   OD023121];  {[}U24 OD023176];  {[}1 U24 OD023163];  {[}3 OT2 OD023205]; 
   {[}3 OT2 OD023206];  {[}1 OT2 OD025277]},
Funding-Text = {This research was funded by the National Institutes of Health (NIH)
   Agreement OTA OT2HL161847 as part of the Researching COVID to Enhance
   Recovery (RECOVER) research program, as well as CD2H- The National COVID
   Cohort Collaborative (N3C) U24TR002306. The All of Us Research Program
   is supported by the National Institutes of Health, Office of the
   Director: Regional Medical Centers (1 OT2 OD026549; 1 OT2 OD026554; 1
   OT2 OD026557; 1 OT2 OD026556; 1 OT2 OD026550; 1 OT2 OD 026552; 1 OT2
   OD026553; 1 OT2 OD026548; 1 OT2 OD026551; 1 OT2 OD026555; IAA: AOD21037,
   AOD22003, AOD16037, AOD21041), Federally Qualified Health Centers (HHSN
   263201600085U), Data and Research Center (5 U2C OD023196), Biobank (1
   U24 OD023121), The Participant Center (U24 OD023176), Participant
   Technology Systems Center (1 U24 OD023163), Communications and
   Engagement (3 OT2 OD023205; 3 OT2 OD023206), and Community Partners (1
   OT2 OD025277; 3 OT2 OD025315; 1 OT2 OD025337; 1 OT2 OD025276).},
Number-of-Cited-References = {17},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {J. Am. Med. Inf. Assoc.},
Doc-Delivery-Number = {K3DM5},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000992407100001},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000809040700001,
Author = {Uribe, S. E. and Sofi-Mahmudi, A. and Raittio, E. and Maldupa, I and
   Vilne, B.},
Title = {Dental Research Data Availability and Quality According to the FAIR
   Principles},
Journal = {JOURNAL OF DENTAL RESEARCH},
Year = {2022},
Volume = {101},
Number = {11, SI},
Pages = {1307-1313},
Month = {OCT},
Abstract = {According to the FAIR principles, data produced by scientific research
   should be findable, accessible, interoperable, and reusable-for
   instance, to be used in machine learning algorithms. However, to date,
   there is no estimate of the quantity or quality of dental research data
   evaluated via the FAIR principles. We aimed to determine the
   availability of open data in dental research and to assess compliance
   with the FAIR principles (or FAIRness) of shared dental research data.
   We downloaded all available articles published in PubMed-indexed dental
   journals from 2016 to 2021 as open access from Europe PubMed Central. In
   addition, we took a random sample of 500 dental articles that were not
   open access through Europe PubMed Central. We assessed data sharing in
   the articles and compliance of shared data to the FAIR principles
   programmatically. Results showed that of 7,509 investigated articles,
   112 (1.5\%) shared data. The average (SD) level of compliance with the
   FAIR metrics was 32.6\% (31.9\%). The average for each metric was as
   follows: findability, 3.4 (2.7) of 7; accessibility, 1.0 (1.0) of 3;
   interoperability, 1.1 (1.2) of 4; and reusability, 2.4 (2.6) of 10. No
   considerable changes in data sharing or quality of shared data occurred
   over the years. Our findings indicated that dental researchers rarely
   shared data, and when they did share, the FAIR quality was suboptimal.
   Machine learning algorithms could understand 1\% of available dental
   research data. These undermine the reproducibility of dental research
   and hinder gaining the knowledge that can be gleaned from machine
   learning algorithms and applications.},
Publisher = {SAGE PUBLICATIONS INC},
Address = {2455 TELLER RD, THOUSAND OAKS, CA 91320 USA},
Type = {Article},
Language = {English},
Affiliation = {Uribe, SE (Corresponding Author), Riga Stradins Univ, Dept Conservat Dent \& Oral Hlth, Dzirciema Iela 20 Off 248, LV-1007 Riga, Latvia.
   Uribe, S. E.; Vilne, B., Riga Stradins Univ, Bioinformat Lab, Riga, Latvia.
   Uribe, S. E.; Maldupa, I, Riga Stradins Univ, Dept Conservat Dent \& Oral Hlth, Dzirciema Iela 20 Off 248, LV-1007 Riga, Latvia.
   Uribe, S. E., Univ Austral Chile, Sch Dent, Valdivia, Chile.
   Uribe, S. E., Riga Tech Univ, Baltic Biomat Ctr Excellence, Riga, Latvia.
   Sofi-Mahmudi, A., Kurdistan Univ Med Sci, Seqiz Hlth Network, Seqiz, Kurdistan, Iran.
   Sofi-Mahmudi, A., Natl Inst Med Res Dev, Cochrane Iran Associate Ctr, Tehran, Iran.
   Raittio, E., Univ Eastern Finland, Inst Dent, Kuopio, Finland.},
DOI = {10.1177/00220345221101321},
EarlyAccessDate = {JUN 2022},
Article-Number = {00220345221101321},
ISSN = {0022-0345},
EISSN = {1544-0591},
Keywords = {deep learning; machine learning; open data; dental informatics;
   electronic dental records; outcomes research},
Research-Areas = {Dentistry, Oral Surgery \& Medicine},
Web-of-Science-Categories  = {Dentistry, Oral Surgery \& Medicine},
Author-Email = {sergio.uribe@rsu.lv},
Affiliations = {Riga Stradins University; Riga Stradins University; Universidad Austral
   de Chile; Riga Technical University; Kurdistan University of Medical
   Sciences; University of Eastern Finland},
ResearcherID-Numbers = {Uribe, Sergio E./C-9579-2011
   VILNE, BAIBA/GQZ-2721-2022
   Maldupa, Ilze/AAA-3514-2021
   Sofi-Mahmudi, Ahmad/AAO-5069-2021
   Raittio, Eero/AAA-8012-2021},
ORCID-Numbers = {Uribe, Sergio E./0000-0003-0684-2025
   VILNE, BAIBA/0000-0002-1084-7067
   Maldupa, Ilze/0000-0002-5967-956X
   Sofi-Mahmudi, Ahmad/0000-0001-6829-0823
   Raittio, Eero/0000-0002-9258-9355},
Funding-Acknowledgement = {European Union {[}857287]},
Funding-Text = {The authors disclosed receipt of the following financial support for the
   research, authorship, and/or publication of this article: This research
   was funded by MikroTik-RSU to S.E. Uribe (toward implementing the RSU
   data repository and the FAIR data management principles). S.E. Uribe
   also acknowledges financial support from the European Union's Horizon
   2020 Research and Innovation Programme (grant 857287).},
Number-of-Cited-References = {40},
Times-Cited = {4},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {12},
Journal-ISO = {J. Dent. Res.},
Doc-Delivery-Number = {4X6TU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000809040700001},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000486393800022,
Author = {Moreno, Antonio and Torre, Doroteo and Valverde, Ana and Campillos,
   Leonardo},
Title = {Report on reusable documents as language resources in Spain, under the
   Government Plan for Language Technologies},
Journal = {PROCESAMIENTO DEL LENGUAJE NATURAL},
Year = {2019},
Number = {63},
Pages = {167-170},
Month = {SEP},
Abstract = {This report was carried out within the Spanish administration-driven
   initiative Language Technologies Plan (Plan TL), funded by Secretaria de
   Estado para el Avance Digital and Red.es. The main goals are collecting
   from Spanish public administrations a listing of provided resources and
   open data that can be transformed to language resources, as well as
   proposing an action plan to process and distribute them. We designed a
   specific methodology for listing and evaluating the degree of maturity
   of the considered data. We created two listings: a preliminary
   collection of 101 resources, and 24 resources and data repositories
   selected from the first list for a detailed analysis and evaluation.
   This report also features a comparative analysis of similar initiatives
   and studies conducted abroad. We conclude with generic recommendations
   and detailed strategies for the selected resources. The report and
   listings are publicly available at Red.es and the Plan TL. website.},
Publisher = {SOC ESPANOLA PROCESAMIENTO LENGUAJE NATURAL-SEPLN},
Address = {DEPT LENGUAJES \& SISTEMAS INFORMATICOS, UNIV ALICANTE, APDO 99,
   ALICANTE, 03080, SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {Moreno, A (Corresponding Author), Univ Autonoma Madrid, Madrid, Spain.
   Moreno, Antonio; Torre, Doroteo; Valverde, Ana; Campillos, Leonardo, Univ Autonoma Madrid, Madrid, Spain.
   Campillos, Leonardo, CNRS, LIMSI, Orsay, France.
   Valverde, Ana, Real Acad Nacl Med, Madrid, Spain.},
DOI = {10.26342/2019-63-22},
ISSN = {1135-5948},
EISSN = {1989-7553},
Keywords = {language resources; Plan TL; Spanish public administrations; Open Data;
   Public Sector Information; PSI},
Research-Areas = {Linguistics},
Web-of-Science-Categories  = {Linguistics},
Author-Email = {antonio.msandoval@uam.es
   doroteo.torre@uam.es
   avalverde@ranm.es
   leonardo.campillos@uam.es},
Affiliations = {Autonomous University of Madrid; Centre National de la Recherche
   Scientifique (CNRS); Universite Paris Saclay},
ResearcherID-Numbers = {Toledano, Doroteo T/C-7750-2014
   Moreno-Sandoval, Antonio/ABG-5917-2020
   Moreno-Sandoval, Antonio/B-5429-2010},
ORCID-Numbers = {Toledano, Doroteo T/0000-0003-1159-6455
   Moreno-Sandoval, Antonio/0000-0002-9029-2216
   Moreno-Sandoval, Antonio/0000-0002-9029-2216},
Number-of-Cited-References = {2},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Proces. Leng. Nat.},
Doc-Delivery-Number = {IY4WN},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000486393800022},
DA = {2024-01-15},
}

@article{ WOS:000774681400001,
Author = {Fanelli, Rosa Maria},
Title = {Bridging the Gender Gap in the Agricultural Sector: Evidence from
   European Union Countries},
Journal = {SOCIAL SCIENCES-BASEL},
Year = {2022},
Volume = {11},
Number = {3},
Month = {MAR},
Abstract = {In European Union countries most farms are operated by smallholders in
   extensive agriculture and approximately 30\% of agricultural farms are
   operated by woman. Despite the growing importance of the role of women
   in the agricultural sector, a more complete picture of the gender gap
   and the differences between female and male-operated farms is still
   lacking. The principal aim of this paper is to fill this gap by
   highlighting the differences between female and male-operated farms. The
   data used comes from the World Bank Open Data repository and Eurostat.
   The methodology consists of descriptive statistical analysis, principal
   component analysis, and multivariate regression models. The analysis is
   used to investigate how a set of indicators affects the gender gap in
   the agricultural sector. The research questions test how the
   socio-economic determinants and traditional agricultural land use
   influence the historical gender division of labour and the evolution and
   persistence of farm differences. The results from almost all 27 EU
   countries suggest that women, the same as men, can be considered
   ``productive resources{''} and play an important role in the agriculture
   sector in areas such as crop and livestock production. However, their
   activities are less remunerative.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Fanelli, RM (Corresponding Author), Univ Molise, Dept Econ, I-86100 Campobasso, Italy.
   Fanelli, Rosa Maria, Univ Molise, Dept Econ, I-86100 Campobasso, Italy.},
DOI = {10.3390/socsci11030105},
Article-Number = {105},
EISSN = {2076-0760},
Keywords = {agricultural sector; gender gap; multivariate regression models;
   principal component analysis},
Keywords-Plus = {MULTIPLE LINEAR-REGRESSION; EDUCATION; EFFICIENCY},
Research-Areas = {Social Sciences - Other Topics},
Web-of-Science-Categories  = {Social Sciences, Interdisciplinary},
Author-Email = {rfanelli@unimol.it},
Affiliations = {University of Molise},
ORCID-Numbers = {Rosa Maria, Fanelli/0000-0002-0873-6077},
Number-of-Cited-References = {40},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Soc. Sci.-Basel},
Doc-Delivery-Number = {0B5NN},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000774681400001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000419605800005,
Author = {Estiri, Hossein and Stephens, Kari A. and Klann, Jeffrey G. and Murphy,
   Shawn N.},
Title = {Exploring completeness in clinical data research networks with
   DQ<SUP>e</SUP>-c},
Journal = {JOURNAL OF THE AMERICAN MEDICAL INFORMATICS ASSOCIATION},
Year = {2018},
Volume = {25},
Number = {1},
Pages = {17-24},
Month = {JAN},
Abstract = {To provide an open source, interoperable, and scalable data quality
   assessment tool for evaluation and visualization of completeness and
   conformance in electronic health record (EHR) data repositories.
   This article describes the tool's design and architecture and gives an
   overview of its outputs using a sample dataset of 200 000 randomly
   selected patient records with an encounter since January 1, 2010,
   extracted from the Research Patient Data Registry (RPDR) at Partners
   HealthCare. All the code and instructions to run the tool and interpret
   its results are provided in the Supplementary Appendix.
   DQ(e)-c produces a web-based report that summarizes data completeness
   and conformance in a given EHR data repository through descriptive
   graphics and tables. Results from running the tool on the sample RPDR
   data are organized into 4 sections: load and test details, completeness
   test, data model conformance test, and test of missingness in key
   clinical indicators.
   Open science, interoperability across major clinical informatics
   platforms, and scalability to large databases are key design
   considerations for DQ(e)-c. Iterative implementation of the tool across
   different institutions directed us to improve the scalability and
   interoperability of the tool and find ways to facilitate local setup.
   EHR data quality assessment has been hampered by implementation of ad
   hoc processes. The architecture and implementation of DQ(e)-c offer
   valuable insights for developing reproducible and scalable data science
   tools to assess, manage, and process data in clinical data repositories.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Estiri, H (Corresponding Author), MGH, Comp Sci Lab, 50 Staniford St,Suite 750, Boston, MA 02114 USA.
   Estiri, Hossein; Klann, Jeffrey G.; Murphy, Shawn N., Harvard Med Sch, Boston, MA USA.
   Estiri, Hossein; Klann, Jeffrey G.; Murphy, Shawn N., Massachusetts Gen Hosp, Boston, MA 02114 USA.
   Estiri, Hossein; Klann, Jeffrey G.; Murphy, Shawn N., Partners HealthCare, Boston, MA USA.
   Stephens, Kari A., Univ Washington, Dept Biomed Informat \& Med Educ, Seattle, WA 98195 USA.
   Stephens, Kari A., Univ Washington, Dept Psychiat \& Behav Sci, Seattle, WA 98195 USA.},
DOI = {10.1093/jamia/ocx109},
ISSN = {1067-5027},
EISSN = {1527-974X},
Keywords = {data quality; electronic health records; data science; medical
   informatics applications},
Keywords-Plus = {ELECTRONIC HEALTH RECORD; DATA QUALITY ASSESSMENT; BIG DATA; BIOMEDICAL
   DATA; INFORMATICS; ACCURACY; CARE},
Research-Areas = {Computer Science; Health Care Sciences \& Services; Information Science
   \& Library Science; Medical Informatics},
Web-of-Science-Categories  = {Computer Science, Information Systems; Computer Science,
   Interdisciplinary Applications; Health Care Sciences \& Services;
   Information Science \& Library Science; Medical Informatics},
Author-Email = {hestiri@mgh.harvard.edu},
Affiliations = {Harvard University; Harvard Medical School; Harvard University;
   Massachusetts General Hospital; Partners Healthcare System; University
   of Washington; University of Washington Seattle; University of
   Washington; University of Washington Seattle},
ResearcherID-Numbers = {, 叶叶叶/ABE-1619-2020},
Funding-Acknowledgement = {Patient-Centered Outcomes Research Institute (PCORI) Award
   {[}CDRN-1306-04608]; NIH NCATS {[}UL1TR000423]; CDC {[}200-2015-87699];
   NIH {[}R01-HG009174]; NLM training grant {[}T15LM007092]},
Funding-Text = {This work was partially funded through a Patient-Centered Outcomes
   Research Institute (PCORI) Award (CDRN-1306-04608) for development of
   the National Patient-Centered Clinical Research Network, known as
   PCOR-net, NIH NCATS award UL1TR000423, CDC (200-2015-87699), NIH
   R01-HG009174, and NLM training grant T15LM007092.},
Number-of-Cited-References = {40},
Times-Cited = {11},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {20},
Journal-ISO = {J. Am. Med. Inf. Assoc.},
Doc-Delivery-Number = {FS2JX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000419605800005},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000392925800010,
Author = {Kroon-Batenburg, Loes M. J. and Helliwell, John R. and McMahon, Brian
   and Terwilliger, Thomas C.},
Title = {Raw diffraction data preservation and reuse: overview, update on
   practicalities and metadata requirements},
Journal = {IUCRJ},
Year = {2017},
Volume = {4},
Number = {1},
Pages = {87-99},
Month = {JAN},
Abstract = {A topical review is presented of the rapidly developing interest in and
   storage options for the preservation and reuse of raw data within the
   scientific domain of the IUCr and its Commissions, each of which
   operates within a great diversity of instrumentation. A resume is
   included of the case for raw diffraction data deposition. An overall
   context is set by highlighting the initiatives of science policy makers
   towards an `Open Science' model within which crystallographers will
   increasingly work in the future; this will bring new funding
   opportunities but also new codes of procedure within open science
   frameworks. Skills education and training for crystallographers will
   need to be expanded. Overall, there are now the means and the
   organization for the preservation of raw crystallographic diffraction
   data via different types of archive, such as at universities,
   disciplinespecific repositories (Integrated Resource for Reproducibility
   in Macromolecular Crystallography, Structural Biology Data Grid),
   general public data repositories (Zenodo, ResearchGate) and centralized
   neutron and X-ray facilities. Formulation of improved metadata
   descriptors for the raw data types of each of the IUCr Commissions is in
   progress; some detailed examples are provided. A number of specific case
   studies are presented, including an example research thread that
   provides complete open access to raw data.},
Publisher = {INT UNION CRYSTALLOGRAPHY},
Address = {2 ABBEY SQ, CHESTER, CH1 2HU, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Helliwell, JR (Corresponding Author), Univ Manchester, Fac Engn \& Phys Sci, Sch Chem, Brunswick St, Manchester M13 9PL, Lancs, England.
   Kroon-Batenburg, Loes M. J., Univ Utrecht, Bijvoet Ctr Biomol Res, Crystal \& Struct Chem, Padualaan 8, NL-3584 CH Utrecht, Netherlands.
   Helliwell, John R., Univ Manchester, Fac Engn \& Phys Sci, Sch Chem, Brunswick St, Manchester M13 9PL, Lancs, England.
   McMahon, Brian, Int Union Crystallog, 5 Abbey Sq, Chester CH1 2HU, Cheshire, England.
   Terwilliger, Thomas C., Los Alamos Natl Lab, Biosci Div, Mail Stop M888, Los Alamos, NM 87507 USA.},
DOI = {10.1107/S2052252516018315},
ISSN = {2052-2525},
Keywords = {raw diffraction data; data archiving; metadata descriptors for raw data;
   diversity of crystallographic instrumentation},
Keywords-Plus = {STRUCTURAL BIOLOGY; CAUTIONARY-TALE; ALWAYS-GO; CRYSTALLOGRAPHY;
   CISPLATIN; FORMAT; PUBLICATION; CARBOPLATIN; EXPERIENCES; DEPOSITION},
Research-Areas = {Chemistry; Crystallography; Materials Science},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary; Crystallography; Materials Science,
   Multidisciplinary},
Author-Email = {john.helliwell@manchester.ac.uk},
Affiliations = {Utrecht University; University of Manchester; United States Department
   of Energy (DOE); Los Alamos National Laboratory},
ResearcherID-Numbers = {Helliwell, John R/C-4587-2014
   Terwilliger, Thomas C/K-4109-2012
   Terwilliger, Thomas/AAM-4079-2020
   Terwilliger, Thomas/AEF-4827-2022
   },
ORCID-Numbers = {Helliwell, John R/0000-0002-0520-7540
   Terwilliger, Thomas C/0000-0001-6384-0320
   Terwilliger, Thomas/0000-0001-6384-0320
   McMahon, Brian/0000-0003-0391-0002},
Number-of-Cited-References = {49},
Times-Cited = {30},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {29},
Journal-ISO = {IUCrJ},
Doc-Delivery-Number = {EJ0UK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000392925800010},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000944930900001,
Author = {Branda, Francesco and Mahal, Ahmed and Maruotti, Antonello and Pierini,
   Massimo and Mazzoli, Sandra},
Title = {The challenges of open data for future epidemic preparedness: The
   experience of the 2022 Ebolavirus outbreak in Uganda},
Journal = {FRONTIERS IN PHARMACOLOGY},
Year = {2023},
Volume = {14},
Month = {FEB 10},
Abstract = {On 20 September 2022, the Ministry of Health in Uganda, together with
   the World Health Organization-Regional Office for Africa (WHO AFRO)
   confirmed an outbreak of EVD due to Sudan ebolavirus in Mubende
   District, after one fatal case was confirmed. Real-time information are
   needed to provide crucial information to understand transmissibility,
   risk of geographical spread, routes of transmission, risk factors of
   infection, and provide the basis for epidemiological modelling that can
   inform response and containment planning to reduce the burden of
   disease. We made an effort to build a centralized repository of the
   Ebola virus cases from verified sources, providing information on dates
   of symptom onset, locations (aggregated to the district level), and when
   available, the gender and status of hospitals, reporting bed capacity
   and isolation unit occupancy rate according to the severity status of
   the patient. The proposed data repository provides researchers and
   policymakers timely, complete, and easy-accessible data to monitor the
   most recent trends of the Ebola outbreak in Ugandan districts with
   informative graphical outputs. This favors a rapid global response to
   the disease, enabling governments to prioritize and adjust their
   decisions quickly and effectively in response to the rapidly evolving
   emergency, with a solid data basis.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Branda, F (Corresponding Author), Univ Calabria, Dept Comp Sci Modeling Elect \& Syst Engn DIMES, Arcavacata Di Rende, Italy.
   Branda, Francesco, Univ Calabria, Dept Comp Sci Modeling Elect \& Syst Engn DIMES, Arcavacata Di Rende, Italy.
   Mahal, Ahmed, Cihan Univ Erbil, Coll Hlth Technol, Dept Med Biochem Anal, Erbil, Iraq.
   Maruotti, Antonello, Libera Univ Ss Maria Assunta, Dept GEPLI, Rome, Italy.
   Pierini, Massimo; Mazzoli, Sandra, EpiData it, Bergamo, Italy.
   Pierini, Massimo, Univ Mercatorum, Stat \& Big Data, Rome, Italy.
   Mazzoli, Sandra, St Maria Annunziata Hosp, STDs Ctr, Florence, Italy.},
DOI = {10.3389/fphar.2023.1101894},
Article-Number = {1101894},
EISSN = {1663-9812},
Keywords = {Uganda; viral infections; Ebola virus; infection control; outbreaks;
   surveillance; epidemiology},
Research-Areas = {Pharmacology \& Pharmacy},
Web-of-Science-Categories  = {Pharmacology \& Pharmacy},
Author-Email = {francesco.branda@unical.it},
Affiliations = {University of Calabria; Cihan University-Erbil; Universita Telematica
   Mercatorum},
ResearcherID-Numbers = {Mahal, Ahmed/GPS-4935-2022
   Branda, Francesco/AAV-4142-2021},
ORCID-Numbers = {Mahal, Ahmed/0000-0002-6977-3752
   Branda, Francesco/0000-0002-9485-3877},
Number-of-Cited-References = {21},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Front. Pharmacol.},
Doc-Delivery-Number = {9Q4IW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000944930900001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000844531500001,
Author = {Lortie, C. J. and Poulsen, Camila Vargas and Brun, Julien and Kui, Li},
Title = {Tabular strategies for metadata in ecology, evolution, and the
   environmental sciences},
Journal = {ECOLOGY AND EVOLUTION},
Year = {2022},
Volume = {12},
Number = {8},
Month = {AUG},
Abstract = {Data support knowledge development and theory advances in ecology and
   evolution. We are increasingly reusing data within our teams and
   projects and through the global, openly archived datasets of others.
   Metadata can be challenging to write and interpret, but it is always
   crucial for reuse. The value metadata cannot be overstated-even as a
   relatively independent research object because it describes the work
   that has been done in a structured format. We advance a new perspective
   and classify methods for metadata curation and development with tables.
   Tables with templates can be effectively used to capture all components
   of an experiment or project in a single, easy-to-read file familiar to
   most scientists. If coupled with the R programming language, metadata
   from tables can then be rapidly and reproducibly converted to
   publication formats including extensible markup language files suitable
   for data repositories. Tables can also be used to summarize existing
   metadata and store metadata across many datasets. A case study is
   provided and the added benefits of tables for metadata, a priori, are
   developed to ensure a more streamlined publishing process for many data
   repositories used in ecology, evolution, and the environmental sciences.
   In ecology and evolution, researchers are often highly tabular thinkers
   from experimental data collection in the lab and/or field, and
   representations of metadata as a table will provide novel research and
   reuse insights.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Lortie, CJ (Corresponding Author), UCSB, Natl Ctr Ecol Anal \& Synth, Santa Barbara, CA 93106 USA.
   Lortie, C. J.; Brun, Julien, UCSB, Natl Ctr Ecol Anal \& Synth, Santa Barbara, CA 93106 USA.
   Lortie, C. J., York Univ, Dept Biol, Toronto, ON, Canada.
   Poulsen, Camila Vargas; Kui, Li, UCSB, Marine Sci Inst, Santa Barbara, CA USA.},
DOI = {10.1002/ece3.9245},
Article-Number = {e9245},
ISSN = {2045-7758},
Keywords = {data; metadata; open science; R programming language; tables; template;
   workflows},
Research-Areas = {Environmental Sciences \& Ecology; Evolutionary Biology},
Web-of-Science-Categories  = {Ecology; Evolutionary Biology},
Author-Email = {lortie@nceas.ucsb.edu},
Affiliations = {University of California System; University of California Santa Barbara;
   National Center for Ecological Analysis \& Synthesis; York University -
   Canada; University of California System; University of California Santa
   Barbara},
ResearcherID-Numbers = {Brun, Julien/C-9618-2009},
Funding-Acknowledgement = {NSERC DG},
Funding-Text = {CJL was funded by an NSERC DG.},
Number-of-Cited-References = {39},
Times-Cited = {0},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Ecol. Evol.},
Doc-Delivery-Number = {3Z6MJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000844531500001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000397963400011,
Author = {Buch, Ethan R. and Santarnecchi, Emiliano and Antal, Andrea and Born,
   Jan and Celnik, Pablo A. and Classen, Joseph and Gerloff, Christian and
   Hallett, Mark and Hummel, Friedhelm C. and Nitsche, Michael A. and
   Pascual-Leone, Alvaro and Paulus, Walter J. and Reis, Janine and
   Robertson, Edwin M. and Rothwell, John C. and Sandrini, Marco and
   Schambra, Heidi M. and Wassermann, Eric M. and Ziemann, Ulf and Cohen,
   Leonardo G.},
Title = {Effects of tDCS on motor learning and memory formation: A consensus and
   critical position paper},
Journal = {CLINICAL NEUROPHYSIOLOGY},
Year = {2017},
Volume = {128},
Number = {4},
Pages = {589-603},
Month = {APR},
Abstract = {Motor skills are required for activities of daily living. Transcranial
   direct current stimulation (tDCS) applied in association with motor
   skill learning has been investigated as a tool for enhancing training
   effects in health and disease. Here, we review the published literature
   investigating whether tDCS can facilitate the acquisition, retention or
   adaptation of motor skills. Work in multiple laboratories is under-way
   to develop a mechanistic understanding of tDCS effects on different
   forms of learning and to optimize stimulation protocols. Efforts are
   required to improve reproducibility and standardization. Overall,
   reproducibility remains to be fully tested, effect sizes with present
   techniques vary over a wide range, and the basis of observed
   inter-individual variability in tDCS effects is incompletely understood.
   It is recommended that future studies explicitly state in the Methods
   the exploratory (hypothesis-generating) or hypothesis-driven
   (confirmatory) nature of the experimental designs. General research
   practices could be improved with prospective pre-registration of
   hypothesis-based investigations, more emphasis on the detailed
   description of methods (including all pertinent details to enable future
   modeling of induced current and experimental replication), and use of
   post-publication open data repositories. A checklist is proposed for
   reporting tDCS investigations in a way that can improve efforts to
   assess reproducibility. (C) 2017 Published by Elsevier Ireland Ltd on
   behalf of International Federation of Clinical Neurophysiology.},
Publisher = {ELSEVIER IRELAND LTD},
Address = {ELSEVIER HOUSE, BROOKVALE PLAZA, EAST PARK SHANNON, CO, CLARE, 00000,
   IRELAND},
Type = {Article},
Language = {English},
Affiliation = {Cohen, LG (Corresponding Author), Natl Inst Hlth, Natl Inst Neurol Disorders \& Stroke, Human Cort Physiol \& Neurorehabilitat Sect, BG 10 RM 7D54 MSC 1428,10 Ctr, Bethesda, MD 20892 USA.
   Buch, Ethan R.; Cohen, Leonardo G., Natl Inst Hlth, Natl Inst Neurol Disorders \& Stroke, Human Cort Physiol \& Neurorehabilitat Sect, BG 10 RM 7D54 MSC 1428,10 Ctr, Bethesda, MD 20892 USA.
   Santarnecchi, Emiliano; Pascual-Leone, Alvaro, Harvard Med Sch, Beth Israel Med Ctr, Dept Neurol, Div Cognit Neurol,Berenson Allen Ctr Non Invas, Boston, MA USA.
   Antal, Andrea; Paulus, Walter J., Georg August Univ, Univ Med Ctr, Dept Clin Neurophysiol, Gottingen, Germany.
   Born, Jan, Univ Tubingen, Inst Med Psychol, Behav Neurobiol, Tubingen, Germany.
   Born, Jan, Univ Tubingen, Ctr Integrat Neurosci, Tubingen, Germany.
   Celnik, Pablo A., Johns Hopkins Med Inst, Dept Phys Med \& Rehabil, Baltimore, MD USA.
   Celnik, Pablo A., Johns Hopkins Med Inst, Dept Neurosci, Baltimore, MD USA.
   Classen, Joseph, Univ Leipzig, Dept Neurol, Leipzig, Germany.
   Gerloff, Christian; Hummel, Friedhelm C., Univ Med Ctr Hamburg Eppendorf, Dept Neurol, Brain Imaging \& NeuroStimulat BINS Lab, Hamburg, Germany.
   Hallett, Mark, Natl Inst Neurol Disorders \& Stroke, Human Motor Control Sect, Bethesda, MD USA.
   Nitsche, Michael A., Dept Psychol \& Neurosci, Leibniz Res Ctr Working Environm \& Human Factors, Dortmund, Germany.
   Reis, Janine, Albert Ludwigs Univ, Dept Neurol, Freiburg, Germany.
   Robertson, Edwin M., Univ Glasgow, Inst Neurosci \& Psychol, Glasgow, Lanark, Scotland.
   Rothwell, John C., UCL Inst Neurol, Queen Sq, London, England.
   Sandrini, Marco, Univ Roehampton, Dept Psychol, London, England.
   Schambra, Heidi M., Columbia Univ, Dept Rehabil \& Regenerat Med, New York, NY USA.
   Wassermann, Eric M., Natl Inst Hlth, Natl Inst Neurol Disorders \& Stroke, Behav Neurol Unit, Bethesda, MD USA.
   Ziemann, Ulf, Eberhard Karls Univ Tubingen, Hertie Inst Clin Brain Res, Dept Neurol Stroke, Tubingen, Germany.},
DOI = {10.1016/j.clinph.2017.01.004},
ISSN = {1388-2457},
EISSN = {1872-8952},
Keywords = {tDCS; Non-invasive brain stimulation; Motor; Learning; Memory; Open
   Science; Effect-size; Guidelines},
Keywords-Plus = {DIRECT-CURRENT STIMULATION; TRANSCRANIAL MAGNETIC STIMULATION;
   NONINVASIVE BRAIN-STIMULATION; MEP AMPLITUDE-MODULATION; INDUCED
   MOVEMENT THERAPY; HEALTHY-HUMAN SUBJECTS; PREMOTOR CORTEX; CHRONIC
   STROKE; CORTICAL EXCITABILITY; SKILL ACQUISITION},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Clinical Neurology; Neurosciences},
Author-Email = {CohenL@ninds.nih.gov},
Affiliations = {National Institutes of Health (NIH) - USA; NIH National Institute of
   Neurological Disorders \& Stroke (NINDS); Harvard University; Beth
   Israel Deaconess Medical Center; Harvard Medical School; University of
   Gottingen; Eberhard Karls University of Tubingen; Eberhard Karls
   University of Tubingen; Johns Hopkins University; Johns Hopkins
   Medicine; Johns Hopkins University; Johns Hopkins Medicine; Leipzig
   University; University of Hamburg; University Medical Center
   Hamburg-Eppendorf; National Institutes of Health (NIH) - USA; NIH
   National Institute of Neurological Disorders \& Stroke (NINDS); Dortmund
   University of Technology; Leibniz Institut for Arbeitsforschung an der
   TU Dortmund (IFADO); University of Freiburg; University of Glasgow;
   University of London; University College London; Roehampton University;
   Columbia University; National Institutes of Health (NIH) - USA; NIH
   National Institute of Neurological Disorders \& Stroke (NINDS); Eberhard
   Karls University of Tubingen; Eberhard Karls University Hospital},
ResearcherID-Numbers = {Buch, Ethan/AAB-4549-2021
   Paulus, Walter/A-3544-2009
   Born, Jan/K-2596-2016
   Sandrini, Marco/J-2276-2014
   Nitsche, Michael A/B-6755-2012
   Wassermann, Eric/AAC-9064-2020
   Ziemann, Ulf/AAY-9125-2020
   Hummel, Friedhelm/AGS-7403-2022
   Classen, Joseph/AAB-1337-2022
   Santarnecchi, Emiliano/H-7528-2017
   Pascual-Leone, Alvaro/AAC-5101-2019},
ORCID-Numbers = {Paulus, Walter/0000-0001-5549-8377
   Born, Jan/0000-0002-1847-6248
   Sandrini, Marco/0000-0002-1664-5722
   Nitsche, Michael A/0000-0002-2207-5965
   Wassermann, Eric/0000-0003-0628-0210
   Hummel, Friedhelm/0000-0002-4746-4633
   Classen, Joseph/0000-0001-7182-6967
   Santarnecchi, Emiliano/0000-0002-6533-7427
   Pascual-Leone, Alvaro/0000-0001-8975-0382},
Funding-Acknowledgement = {Intramural Research Program of the National Institute of Neurological
   Disorders and Stroke},
Funding-Text = {This work was supported by the Intramural Research Program of the
   National Institute of Neurological Disorders and Stroke.},
Number-of-Cited-References = {170},
Times-Cited = {201},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {102},
Journal-ISO = {Clin. Neurophysiol.},
Doc-Delivery-Number = {EQ3HV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000397963400011},
OA = {Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000475287900014,
Author = {Jefferies, Neil and Murphy, Fiona and Ranganathan, Anusha and Murray,
   Hollydawn},
Title = {Data2paper: Giving Researchers Credit for Their Data},
Journal = {PUBLICATIONS},
Year = {2019},
Volume = {7},
Number = {2},
Month = {JUN},
Abstract = {Initially funded as part of the Jisc Data Spring Initiative, a team of
   stakeholders (publishers, data repository managers, coders) has
   developed a simple workflow to streamline data paper submission.
   Metadata about a dataset in a data repository is combined with ORCID
   metadata about the author to automate and thus greatly reduce the
   friction of the submission process. Funders are becoming more interested
   in good data management practice, and institutions are developing
   repositories to hold the data outputs of their researchers, reducing the
   individual burden of data archiving. However, to date only a subset of
   the data produced is associated with publications and thus reliably
   archived, shared and re-used. This represents a loss of knowledge,
   leading to the repetition of research (especially in the case of
   negative observations) and wastes resources. It is laborious for
   time-poor researchers to fully describe their data via an associated
   article to maximise its utility to others, and there is little incentive
   for them to do so. Filling out diverse submission forms, for the
   repository and journal(s), makes things even lengthier. The app makes
   the process of associating and publishing data with a detailed
   description easier, with corresponding citation potential and credit
   benefits.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Jefferies, N (Corresponding Author), Univ Oxford, Bodleian Lib, Oxford OX2 0EW, England.
   Jefferies, Neil, Univ Oxford, Bodleian Lib, Oxford OX2 0EW, England.
   Murphy, Fiona, Univ Reading, Dept Meteorol, Reading RG6 6AS, Berks, England.
   Ranganathan, Anusha, Digital Nest Ltd, Oxford OX1 3LE, England.
   Murray, Hollydawn, F1000Res, London W1T 4LB, England.},
DOI = {10.3390/publications7020036},
Article-Number = {36},
ISSN = {2304-6775},
Keywords = {data papers; publication; open data; credit},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {neil.jefferies@bodleian.ox.ac.uk
   f.murphy@reading.ac.uk
   anusha@digitalnest.co.uk
   hollydawn.murray@f1000.com},
Affiliations = {University of Oxford; University of Reading},
ORCID-Numbers = {Jefferies, Neil/0000-0003-3311-3741
   Murphy, Fiona/0000-0003-1693-1240
   Murray, Hollydawn/0000-0002-8243-2493},
Funding-Acknowledgement = {JISC; Alfred P. Sloan Foundation {[}2017-9874]; OpenAIRE2020; Microsoft
   Research, Azure for Research Grant},
Funding-Text = {This research was funded by: JISC, Research Data Spring, 4807, Alfred P.
   Sloan Foundation, 2017-9874, OpenAIRE, OpenAIRE2020, and Microsoft
   Research, Azure for Research Grant.},
Number-of-Cited-References = {3},
Times-Cited = {2},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Publications},
Doc-Delivery-Number = {II6FG},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000475287900014},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000997061600001,
Author = {Fu, Jiangyang and Tian, Liang and Zhang, Chengzhi and Li, Jiang},
Title = {Opening research data contributes to the citations of related research
   articles: Evidence from <i>Data in Brief</i>},
Journal = {LEARNED PUBLISHING},
Year = {2023},
Volume = {36},
Number = {3},
Pages = {426-438},
Month = {JUL},
Abstract = {This paper explores the effect of publishing a data paper in the Open
   Access journal Data in Brief (DIB) on the citation counts of the related
   research paper. Using regression analysis, citation content analysis and
   a survey method, we investigate whether research papers with a related
   data paper have higher citation counts and the potential reasons. After
   controlling variables that correlate with the citation counts, research
   papers with a related data paper were found to have higher citation
   counts than those published in the same issue of the same journal. Next,
   we explored the causal relationship between the two variables by
   surveying the corresponding authors of 618 papers who shared datasets in
   DIB from 2014 to 2021. The results show that the authors acknowledge the
   benefits of sharing data in DIB, including citation increase and career
   reputation enhancement. We further explored how the data papers in DIB
   increase the citations of the related research papers by using citation
   content analysis. We found that scientists co-cite the data papers and
   their related research papers for the purpose of reusing the underlying
   data or portraying a better understanding of the underlying data and
   related research articles.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Li, J (Corresponding Author), Nanjing Univ, Sch Informat Management, Nanjing 210032, Peoples R China.
   Fu, Jiangyang; Li, Jiang, Nanjing Univ, Sch Informat Management, Nanjing 210032, Peoples R China.
   Tian, Liang; Zhang, Chengzhi, Nanjing Univ Sci \& Technol, Dept Informat Management, Nanjing 210094, Peoples R China.},
DOI = {10.1002/leap.1551},
EarlyAccessDate = {MAY 2023},
ISSN = {0953-1513},
EISSN = {1741-4857},
Keywords = {citation; citation content analysis; Data in Brief; data repository;
   open research data; survey},
Keywords-Plus = {OPEN SCIENCE; IMPACT; MOTIVATIONS; POLICY; ROLES; TITLE},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {lijiang@nju.edu.cn},
Affiliations = {Nanjing University; Nanjing University of Science \& Technology},
ResearcherID-Numbers = {Li, Jiang/Z-1709-2019
   Zhang, Chengzhi/AAK-9998-2020
   Li, Jiang/JHV-1585-2023
   },
ORCID-Numbers = {Li, Jiang/0000-0001-5769-8647
   Zhang, Chengzhi/0000-0001-9522-2914
   zhang, cheng zhi/0000-0001-8121-4796},
Funding-Acknowledgement = {National Natural Science Foundation of China {[}L2124023, 72074113]},
Funding-Text = {ACKNOWLEDGEMENTS The authors acknowledge the National Natural Science
   Foundation of China (Grant Numbers L2124023 and 72074113) for financial
   support. The authors thank Mr. Zhenyue Zhao for his assistance in
   handling the dataset. The authors thank Mr. Zhen Zhang for his
   assistance in the consistency test. The constructive comments from
   anonymous reviewers and editors are appreciated.},
Number-of-Cited-References = {92},
Times-Cited = {1},
Usage-Count-Last-180-days = {23},
Usage-Count-Since-2013 = {28},
Journal-ISO = {Learn. Publ.},
Doc-Delivery-Number = {L5NX7},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000997061600001},
DA = {2024-01-15},
}

@article{ WOS:000851129900001,
Author = {Yamamoto, Michiro and Curley, James and Hirata, Hitoshi},
Title = {Trends in Open vs. Endoscopic Carpal Tunnel Release: A Comprehensive
   Survey in Japan},
Journal = {JOURNAL OF CLINICAL MEDICINE},
Year = {2022},
Volume = {11},
Number = {17},
Month = {SEP},
Abstract = {We analyzed trends in open and endoscopic carpal tunnel release (CTR)
   from 2014 to 2019 using the National Database of Health Insurance Claims
   and Specific Health Checkups in Japan (NDB). Japan has a universal
   health insurance system and more than 95\% of all claims are searchable
   in the NDB open data repository. The results revealed that nearly 40,000
   CTRs were performed annually in Japan, and open CTR was performed almost
   4 times more often than endoscopic CTR. The crude annual incidence of
   CTR in the general population among people 20 years of age or older was
   32.2 per 100,000. The incidence of open CTR peaked in the 80-84 age
   range for both males and females. The incidence of endoscopic CTR peaked
   at 80-84 years in females and at 75-79 years in males. There was a mild
   correlation coefficient between the endoscopic CTRs and the number of
   hand surgery specialists by prefecture per population (r = 0.32, p =
   0.04). However, the number of hand surgeons per capita by region and
   open CTR per capita was not correlated (r = 0.06, p = 0.67). There were
   about twice as many outpatient as inpatient surgeries, reflecting a
   trend toward ambulatory treatment.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Yamamoto, M (Corresponding Author), Nagoya Univ, Dept Hand Surg, Grad Sch Med, Showa Ku, 65 Tsurumai Cho, Nagoya, Aichi 4668550, Japan.
   Yamamoto, Michiro; Curley, James; Hirata, Hitoshi, Nagoya Univ, Dept Hand Surg, Grad Sch Med, Showa Ku, 65 Tsurumai Cho, Nagoya, Aichi 4668550, Japan.},
DOI = {10.3390/jcm11174966},
Article-Number = {4966},
EISSN = {2077-0383},
Keywords = {carpal tunnel syndrome; carpal tunnel release; trends; Japan},
Keywords-Plus = {OUTCOMES},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {michi-ya@med.nagoya-u.ac.jp},
Affiliations = {Nagoya University},
ORCID-Numbers = {Curley, James/0000-0002-4379-5021},
Number-of-Cited-References = {28},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {J. Clin. Med.},
Doc-Delivery-Number = {4J2WW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000851129900001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000904317500001,
Author = {Haase, Claudia and Pohl, Claudia M.},
Title = {Petrophysical Database for European Pegmatite Exploration-EuroPeg},
Journal = {MINERALS},
Year = {2022},
Volume = {12},
Number = {12},
Month = {DEC},
Abstract = {Granitic pegmatites contain natural concentrations of a variety of raw
   materials invaluable for modern technologies and a green and sustainable
   society. The most abundant ones are silicon for high-purity quartz
   applications, and indispensable lithium for today's batteries. However,
   the exploration of these target materials in Europe is underdeveloped,
   causing high dependencies on non-European supply chains. The European
   Commission Horizon 2020 project GREENPEG (GA no. 869274) is addressing
   the exploration of buried, small-scale pegmatite deposits in Europe
   through the development of innovative new exploration toolsets. One
   component of these toolsets is petrophysical data of pegmatite ores and
   their wall rock. These data are essential to supplement and ground-truth
   non-invasive geophysical investigations and deposit modeling. Both
   important tools in mineral exploration can then be used in a more
   targeted and cost-effective way. Petrophysical parameters measured on
   drill core and field samples and acquired through geophysical borehole
   logging are compiled in the first database for European Pegmatite
   deposits: EuroPeg\_PetroDB. Samples are supplemented with
   meta-information, and the database is comprehensively structured in an
   easy-to-use format. Supporting the initiative of FAIR data, EuroPeg is
   freely accessible on an open data repository. The sample content and
   petrophysical measurements are described, followed by the structure and
   usability of the database.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Haase, C (Corresponding Author), Geol Survey Norway, N-7040 Trondheim, Norway.
   Haase, Claudia, Geol Survey Norway, N-7040 Trondheim, Norway.
   Pohl, Claudia M., Terratec Geophys Serv GmbH \& Co KG, D-79423 Heitersheim, Germany.},
DOI = {10.3390/min12121498},
Article-Number = {1498},
EISSN = {2075-163X},
Keywords = {petrophysics; pegmatite; geophysical logging; density; susceptibility;
   resistivity; gamma ray; mechanical properties; database; FAIR},
Research-Areas = {Geochemistry \& Geophysics; Mineralogy; Mining \& Mineral Processing},
Web-of-Science-Categories  = {Geochemistry \& Geophysics; Mineralogy; Mining \& Mineral Processing},
Author-Email = {claudia.haase@ngu.no},
Affiliations = {Geological Survey of Norway},
Funding-Acknowledgement = {European Commission's Horizon 2020 innovation program;  {[}869274]},
Funding-Text = {This research was funded by the European Commission's Horizon 2020
   innovation program under grant agreement No. 869274, project GREENPEG
   New Exploration Tools for European Pegmatite Green-Tech Resources.},
Number-of-Cited-References = {20},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Minerals},
Doc-Delivery-Number = {7J0ZX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000904317500001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000455899200006,
Author = {Huie, J. Russell and Almeida, Carlos A. and Ferguson, Adam R.},
Title = {Neurotrauma as a big-data problem},
Journal = {CURRENT OPINION IN NEUROLOGY},
Year = {2018},
Volume = {31},
Number = {6},
Pages = {702-708},
Month = {DEC},
Abstract = {Purpose of review The field of neurotrauma research faces a
   reproducibility crisis. In response, research leaders in traumatic brain
   injury (TBI) and spinal cord injury (SCI) are leveraging data curation
   and analytics methods to encourage transparency, and improve the rigor
   and reproducibility. Here we review the current challenges and
   opportunities that come from efforts to transform neurotrauma's big data
   to knowledge. Recent findings Three parallel movements are driving
   data-driven-discovery in neurotrauma. First, large multicenter consortia
   are collecting large quantities of neurotrauma data, refining common
   data elements (CDEs) that can be used across studies. Investigators are
   now testing the validity of CDEs in diverse research settings. Second,
   data sharing initiatives are working to make neurotrauma data findable,
   accessible, interoperable, and reusable (FAIR). These efforts are
   reflected by recent open data repository projects for preclinical and
   clinical neurotrauma. Third, machine learning analytics are allowing
   researchers to uncover novel data-driven-hypotheses and test new
   therapeutics in multidimensional outcome space. We are on the threshold
   of a new era in data collection, curation, and analysis. The next phase
   of big data in neurotrauma research will require responsible data
   stewardship, a culture of data-sharing, and the illumination of `dark
   data'.},
Publisher = {LIPPINCOTT WILLIAMS \& WILKINS},
Address = {TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA, PA 19103 USA},
Type = {Review},
Language = {English},
Affiliation = {Ferguson, AR (Corresponding Author), Univ Calif San Francisco, BASIC, Weill Inst Neurosci, San Francisco, CA 94143 USA.
   Ferguson, AR (Corresponding Author), Zuckerberg San Francisco Gen Hosp, San Francisco, CA 94110 USA.
   Huie, J. Russell; Almeida, Carlos A.; Ferguson, Adam R., Univ Calif San Francisco, BASIC, Weill Inst Neurosci, San Francisco, CA 94143 USA.
   Huie, J. Russell; Almeida, Carlos A.; Ferguson, Adam R., Zuckerberg San Francisco Gen Hosp \& Trauma Ctr, San Francisco, CA USA.
   Ferguson, Adam R., San Francisco Vet Affairs Healthcare Syst, San Francisco, CA USA.},
DOI = {10.1097/WCO.0000000000000614},
ISSN = {1350-7540},
EISSN = {1473-6551},
Keywords = {basic science; data science; long-tail data; precision medicine;
   translation},
Keywords-Plus = {TRAUMATIC BRAIN-INJURY; COMMON DATA ELEMENTS; OUTCOME PREDICTION;
   FUTURE; CARE; KNOWLEDGE; POINTS},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Clinical Neurology; Neurosciences},
Author-Email = {adam.ferguson@ucsf.edu},
Affiliations = {University of California System; University of California San Francisco},
ORCID-Numbers = {Ferguson, Adam/0000-0001-7102-1608},
Funding-Acknowledgement = {NIH {[}NS088475, NS106899]; US Department of Veterans Affairs
   {[}1I01RX002245-01]; Wings for Life {[}WFL-US-006/14]; Craig H. Neilsen
   Foundation},
Funding-Text = {This work was supported by grants from the NIH (NS088475, NS106899 to
   A.R.F.), the US Department of Veterans Affairs (1I01RX002245-01 to
   A.R.F.), Wings for Life (WFL-US-006/14 to A.R.F.) and the Craig H.
   Neilsen Foundation.},
Number-of-Cited-References = {41},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {12},
Journal-ISO = {Curr. Opin. Neurol.},
Doc-Delivery-Number = {HH7GQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000455899200006},
OA = {Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000743472400001,
Author = {Van Meenen, Joris and Leysen, Hanne and Chen, Hongyu and Baccarne, Rudi
   and Walter, Deborah and Martin, Bronwen and Maudsley, Stuart},
Title = {Making Biomedical Sciences publications more accessible for machines},
Journal = {MEDICINE HEALTH CARE AND PHILOSOPHY},
Year = {2022},
Volume = {25},
Number = {2},
Pages = {179-190},
Month = {JUN},
Abstract = {With the rapidly expanding catalogue of scientific publications,
   especially within the Biomedical Sciences field, it is becoming
   increasingly difficult for researchers to search for, read or even
   interpret emerging scientific findings. PubMed, just one of the current
   biomedical data repositories, comprises over 33 million citations for
   biomedical research, and over 2500 publications are added each day. To
   further strengthen the impact biomedical research, we suggest that there
   should be more synergy between publications and machines. By bringing
   machines into the realm of research and publication, we can greatly
   augment the assessment, investigation and cataloging of the biomedical
   literary corpus. The effective application of machine-based manuscript
   assessment and interpretation is now crucial, and potentially stands as
   the most effective way for researchers to comprehend and process the
   tsunami of biomedical data and literature. Many biomedical manuscripts
   are currently published online in poorly searchable document types, with
   figures and data presented in formats that are partially inaccessible to
   machine-based approaches. The structure and format of biomedical
   manuscripts should be adapted to facilitate machine-assisted
   interrogation of this important literary corpus. In this context, it is
   important to embrace the concept that biomedical scientists should also
   write manuscripts that can be read by machines. It is likely that an
   enhanced human-machine synergy in reading biomedical publications will
   greatly enhance biomedical data retrieval and reveal novel insights into
   complex datasets.},
Publisher = {SPRINGER},
Address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Maudsley, S (Corresponding Author), Univ Antwerp, Dept Biomed Sci, Receptor Biol Lab, B-2610 Antwerp, Belgium.
   Van Meenen, Joris; Leysen, Hanne; Walter, Deborah; Maudsley, Stuart, Univ Antwerp, Dept Biomed Sci, Receptor Biol Lab, B-2610 Antwerp, Belgium.
   Van Meenen, Joris, Univ Antwerp, Dept Translat Neurosci, Antwerp Res Grp Ocular Sci, B-2610 Antwerp, Belgium.
   Chen, Hongyu, Weill Cornell Med Coll, New York, NY USA.
   Baccarne, Rudi, Univ Antwerp, Anet Lib Automat, B-2610 Antwerp, Belgium.
   Martin, Bronwen, Univ Antwerp, Fac Pharmaceut Vet \& Biomed Sci, B-2610 Antwerp, Belgium.},
DOI = {10.1007/s11019-022-10069-0},
EarlyAccessDate = {JAN 2022},
ISSN = {1386-7423},
EISSN = {1572-8633},
Keywords = {Interoperability; Machine; Research; Open access; Reproducibility},
Keywords-Plus = {BIG DATA; CLASSIFICATION; CANCER; SOFTWARE; MEDICINE; CARE},
Research-Areas = {Social Sciences - Other Topics; History \& Philosophy of Science},
Web-of-Science-Categories  = {Ethics; History \& Philosophy Of Science},
Author-Email = {stuart.maudsley@uantwerpen.be},
Affiliations = {University of Antwerp; University of Antwerp; Cornell University; Weill
   Cornell Medicine; University of Antwerp; University of Antwerp},
ResearcherID-Numbers = {Chen, Hongyu/JGM-9228-2023
   chen, hongyu/HHS-4314-2022
   },
ORCID-Numbers = {Baccarne, Rudi/0000-0001-9533-4852
   Van Meenen, Joris/0000-0002-1295-2805},
Funding-Acknowledgement = {Fonds Wetenschappelijk Onderzoek {[}42/FA010100/32/6484, 1198020N]},
Funding-Text = {This work is supported by Fonds Wetenschappelijk Onderzoek:
   42/FA010100/32/6484, 1198020N.},
Number-of-Cited-References = {75},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Med. Health Care Philos.},
Doc-Delivery-Number = {1U7EV},
Web-of-Science-Index = {Social Science Citation Index (SSCI); Arts &amp; Humanities Citation Index (A&amp;HCI)},
Unique-ID = {WOS:000743472400001},
DA = {2024-01-15},
}

@article{ WOS:000263948000006,
Author = {Mead, Jennifer A. and Bianco, Luca and Bessant, Conrad},
Title = {Recent developments in public proteomic MS repositories and pipelines},
Journal = {PROTEOMICS},
Year = {2009},
Volume = {9},
Number = {4},
Pages = {861-881},
Month = {FEB},
Abstract = {This article provides an overview of publicly available proteomic data
   repositories in a single document with a particular focus on the latest
   developments, many of which are not announced through traditional
   publications. The review is intended to inform the proteomics
   practitioner of the options for storage and dissemination of their MS/MS
   data in the public domain, and to help those who want to mine proteomic
   data generated by others. The latter area has arguably seen the most
   development in recent times, as repositories have sprouted new tools for
   data analysis, visualisation and experimental design. We also highlight
   key biological datasets available at each repository, including standard
   datasets. Finally, we touch upon areas of significant challenge and
   future directions.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Review},
Language = {English},
Affiliation = {Bessant, C (Corresponding Author), Cranfield Univ, Bldg 63, Cranfield MK43 0AL, Beds, England.
   Mead, Jennifer A.; Bianco, Luca; Bessant, Conrad, Cranfield Univ, Cranfield MK43 0AL, Beds, England.},
DOI = {10.1002/pmic.200800553},
ISSN = {1615-9853},
EISSN = {1615-9861},
Keywords = {Bioinformatics; Data mining; Open access; Peptide identification
   pipelines; Proteomic repositories},
Keywords-Plus = {PROTEIN IDENTIFICATION; MASS; PEPTIDE; DATABASE; SOFTWARE; SPECTRA;
   MODEL; QUANTIFICATION; VALIDATION; PREDICTION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
Author-Email = {c.bessant@cranfield.ac.uk},
Affiliations = {Cranfield University},
ResearcherID-Numbers = {Bessant, Conrad/E-7620-2010
   },
ORCID-Numbers = {Bessant, Conrad/0000-0002-7983-1020
   Cham, Jennifer/0000-0002-7446-222X
   Bianco, Luca/0000-0002-0196-8422},
Funding-Acknowledgement = {GlaxoSmithKline; EPSRC; BBSRC},
Funding-Text = {We are grateful to GlaxoSmithKline, EPSRC and BBSRC for funding the
   authors of this review.},
Number-of-Cited-References = {71},
Times-Cited = {34},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Proteomics},
Doc-Delivery-Number = {415QA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000263948000006},
DA = {2024-01-15},
}

@article{ WOS:000992663100015,
Author = {da Silveira, Lucia and da Silva, Fabiano Couto Correa and Dall'agnoll,
   Ares Barbosa},
Title = {Editorial policies of scientific data in journal in the area of
   communication and information},
Journal = {REVISTA IBERO-AMERICANA DE CIENCIA DA INFORMACAO},
Year = {2023},
Volume = {16},
Number = {1},
Pages = {286-306},
Month = {JAN-APR},
Abstract = {This article investigates the situation of journal policies in the field
   of Communication , Information regarding the aspects of publishing
   scientific data as a requirement of quality and transparency, in order
   to facilitate research practices emerging from the open science
   movement. From the universe of 1,804 journals in Qualis Periodicos
   specialIntscript 46 journals from stratum A1 were selected for analysis.
   The result showed that 52\% of journals adopted editorial policies for
   sharing research data, however, less than half presented guidelines for
   authors on how to cite and credit scientific data. It is concluded that,
   despite the inconsistency observed in the political guidelines aimed at
   authors regarding data citation, persistent identifier and licenses for
   use, reuse, sharing and distribution, journals are trying to follow
   trends in open publications.},
Publisher = {UNIV BRASILIA, DEPT CIENCIA INFORMACAO},
Address = {CAIXA POSTAL 15-3011, BRASILIA, DF 00000, BRAZIL},
Type = {Article},
Language = {English},
Affiliation = {da Silveira, L (Corresponding Author), Univ Fed Rio Grande, Programa Posgrad Comun, Porto Alegre, Rio Grande do S, Brazil.
   da Silveira, Lucia; da Silva, Fabiano Couto Correa; Dall'agnoll, Ares Barbosa, Univ Fed Rio Grande, Programa Posgrad Comun, Porto Alegre, Rio Grande do S, Brazil.},
DOI = {10.26512/rici.v16.n1.2023.42055},
ISSN = {1983-5213},
Keywords = {Scientific Data; Data repository; Editorial policy; Scientific journal},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {luciadasilveiras@gmail.com
   luciadasilveiras@gmail.com
   aresdbarbosa@gmail.com},
Affiliations = {Universidade Federal do Rio Grande},
Number-of-Cited-References = {28},
Times-Cited = {0},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Rev. Ibero-Am. Cienc. Inf.},
Doc-Delivery-Number = {G9ZX7},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000992663100015},
DA = {2024-01-15},
}

@article{ WOS:001115010200001,
Author = {Groehs, Adriane and Silveira, Crislaine Zurilda and de Lima, Elaine
   Maria and Dittrich, Eliane and Matos, Igor Yure Ramos and Ribeiro
   Junior, Divino Ignacio},
Title = {LattesData and the adoption of the FAIR Principles: an analysis using
   the F-UJI Automated FAIR Data Assessment Tool},
Journal = {EM QUESTAO},
Year = {2023},
Volume = {29},
Abstract = {The funding agencies of developed countries have begun to demand the
   open-access deposition of research data, requiring compliance with
   standards that ensure data integrity, completeness, quality, and
   accurate metadata descriptions. As a response to this need, the FAIR
   principles -Findability, Accessibility, Interoperability, and
   Reusability have emerged as guidelines to enhance the reusability of
   research data. With the aim of contributing to these discussions, this
   article sought to assess the adoption of FAIR principles in datasets
   deposited in the LattesData repository, utilizing the F-UJI tool
   developed for automating the analysis of FAIR metrics. Methodologically,
   this is a descriptive research study in which 13 datasets available in
   the LattesData repository were analyzed.The results obtained indicate
   that the ``Findability{''} principle was the most well-addressed in the
   datasets, suggesting that the data can be easily located and identified.
   However, the principles of ``Accessibility,{''} ``Interoperability,{''}
   and ``Reusability{''} require more attention, as not all metrics
   associated with these principles were adequately met. In conclusion, it
   is observed that the LattesData repository has started to adopt the FAIR
   principles, albeit in a preliminary manner. There is a need for policies
   and guidelines to ensure that deposited data can be effectively reused.
   The F-UJI tool has proven to be a practical and straightforward tool for
   use in this context. The utilization of such tools for research data
   management can facilitate the implementation of best practices and the
   deposition of high-quality datasets. The implementation of good
   practices and the deposit of quality data sets.},
Publisher = {UNIV FEDERAL RIO GRANDE SUL, FAC BIBLIOTECONOMIA \& COMUNICACAO},
Address = {RUA RAMIRO BARCELOS, 2705, SALA 519, PORTO ALEGRE, RS 90040-060, BRAZIL},
Type = {Article},
Language = {Portuguese},
Affiliation = {Groehs, A (Corresponding Author), Univ Estado Santa Catarina, Florianopolis, SC, Brazil.
   Groehs, Adriane; Silveira, Crislaine Zurilda; de Lima, Elaine Maria; Dittrich, Eliane; Matos, Igor Yure Ramos; Ribeiro Junior, Divino Ignacio, Univ Estado Santa Catarina, Florianopolis, SC, Brazil.},
DOI = {10.1590/1808-5245.29.130018},
Article-Number = {130018},
ISSN = {1807-8893},
EISSN = {1808-5245},
Keywords = {research data; FAIR principles; data repository},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {adriane.groehs.bibliotecaria@gmail.com
   crislaine.silveira@ufsc.br
   elainelimaedf@gmail.com
   eliane.dittrich@udesc.br
   igor.yure@ufsc.br
   divino.ribeiro@udesc.br},
Affiliations = {Universidade do Estado de Santa Catarina},
ORCID-Numbers = {Silveira, Crislaine Zurilda/0000-0003-3081-9968},
Number-of-Cited-References = {28},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Em. Questao},
Doc-Delivery-Number = {Z9DR0},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001115010200001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000496945900005,
Author = {Travieso Rodriguez, Crispulo and Ferreira Araujo, Ronaldo},
Title = {Methodological issues of open research data: analysis of the datasets
   from SciELO included in <i>Figshare</i>},
Journal = {REVISTA ESPANOLA DE DOCUMENTACION CIENTIFICA},
Year = {2019},
Volume = {42},
Number = {3},
Month = {JUL-SEP},
Abstract = {Open research data represent an opportunity to share scientific
   knowledge and to provide new perspectives for validation and
   dissemination of scientific results. Effective re-use of these data
   implies to know both the research methods applied to obtain them and the
   measures of usage and citation that are sistematically gathered. Based
   on the whole catalogue of open research data (348 datasets) from SciELO
   journals available in Figshare, this study aims to explore their
   research methods and the types of data according to data collection
   techniques and subject categories. It also analyses usage and
   bibliometric indicators, file formats and dataset licensing. Results
   show that quantitative data are more frequent than qualitative data. The
   most usual data were those obtained by observation techniques, followed
   by experimental and derived data. This figures varied according to the
   different scientific areas, but usage indicators came out not to be
   significant for the whole set of data files.},
Publisher = {CONSEJO SUPERIOR INVESTIGACIONES CIENTIFICAS-CSIC},
Address = {VITRUVIO 8, 28006 MADRID, SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {Rodríguez, CT (Corresponding Author), Univ Salamanca, Dpto Bibliotecon \& Documentac, Salamanca, Spain.
   Travieso Rodriguez, Crispulo, Univ Salamanca, Dpto Bibliotecon \& Documentac, Salamanca, Spain.
   Ferreira Araujo, Ronaldo, Univ Fed Alagoas, ICHCA, Maceio, Brazil.},
DOI = {10.3989/redc.2019.3.1597},
Article-Number = {e242},
ISSN = {0210-0614},
EISSN = {1988-4621},
Keywords = {research data; open data; research methods; data description; datasets;
   data usage; data repositories},
Keywords-Plus = {ARTICLE REPORTING STANDARDS; APA PUBLICATIONS; PSYCHOLOGY; JOURNALS;
   SCIENCE},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {ctravieso@usal.es},
Affiliations = {University of Salamanca; Universidade Federal de Alagoas},
ResearcherID-Numbers = {Rodriguez, Crispulo Travieso/B-4355-2017
   Araujo, Ronaldo/C-2863-2014},
ORCID-Numbers = {Araujo, Ronaldo/0000-0003-0778-9561},
Number-of-Cited-References = {46},
Times-Cited = {2},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {25},
Journal-ISO = {Rev. Esp. Doc. Cient.},
Doc-Delivery-Number = {JN5NV},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000496945900005},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000482993900010,
Author = {Peersen, Olve B.},
Title = {A Comprehensive Superposition of Viral Polymerase Structures},
Journal = {VIRUSES-BASEL},
Year = {2019},
Volume = {11},
Number = {8},
Month = {AUG},
Abstract = {Nucleic acid polymerases are essential enzymes that replicate the
   genomes of both RNA and DNA viruses. These enzymes are generally encoded
   by viruses themselves so as to provide biochemical functions and control
   elements that differ from those of the host cell polymerases. The core
   active site structure used by all replicative polymerases is highly
   conserved and composed of two key aspartate residues from the conserved
   motifs A and C, but beyond this there is significant divergence among
   structures. These differences can make it difficult to select which
   portions of structures to align for comparisons, yet there are extended
   structural similarities within different groups of viral polymerases
   that should clearly be considered to generate optimal alignments. This
   manuscript describes a comprehensive structure-based superposition of
   every viral polymerase structure solved thus far based on an
   alignment-tree approach wherein aligned regions grow in complexity as
   similarity among polymerases increases. The result is a set of 646
   structures that have been aligned into a single common orientation. This
   provides a convenient resource for directly comparing viral polymerases
   and illustrating structural conservation among them. It also sets the
   stage for detailed bioinformatics analysis to further assess common
   structural features. The full set of protein data bank (PDB) formatted
   files is publicly available via the Polymerase Structures community page
   at the Zenodo.org open data repository.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Peersen, OB (Corresponding Author), Colorado State Univ, Dept Biochem \& Mol Biol, Ft Collins, CO 80523 USA.
   Peersen, Olve B., Colorado State Univ, Dept Biochem \& Mol Biol, Ft Collins, CO 80523 USA.},
DOI = {10.3390/v11080745},
Article-Number = {745},
EISSN = {1999-4915},
Keywords = {polymerase; structure; structure alignment},
Research-Areas = {Virology},
Web-of-Science-Categories  = {Virology},
Author-Email = {Olve.Peersen@ColoState.edu},
Affiliations = {Colorado State University},
ORCID-Numbers = {Peersen, Olve/0000-0001-6208-2660},
Funding-Acknowledgement = {National Institutes of Health {[}R01 AI 059130]},
Funding-Text = {This work was supported by National Institutes of Health grant R01 AI
   059130 to O.B.P.},
Number-of-Cited-References = {12},
Times-Cited = {29},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Viruses-Basel},
Doc-Delivery-Number = {IT6OG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000482993900010},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000333348500004,
Author = {Greshake, Bastian and Bayer, Philipp E. and Rausch, Helge and Reda,
   Julia},
Title = {openSNP-A Crowdsourced Web Resource for Personal Genomics},
Journal = {PLOS ONE},
Year = {2014},
Volume = {9},
Number = {3},
Month = {MAR 19},
Abstract = {Genome-Wide Association Studies are widely used to correlate phenotypic
   traits with genetic variants. These studies usually compare the genetic
   variation between two groups to single out certain Single Nucleotide
   Polymorphisms ( SNPs) that are linked to a phenotypic variation in one
   of the groups. However, it is necessary to have a large enough sample
   size to find statistically significant correlations. Direct-To-Consumer
   (DTC) genetic testing can supply additional data: DTC-companies offer
   the analysis of a large amount of SNPs for an individual at low cost
   without the need to consult a physician or geneticist. Over 100,000
   people have already been genotyped through Direct-To-Consumer genetic
   testing companies. However, this data is not public for a variety of
   reasons and thus cannot be used in research. It seems reasonable to
   create a central open data repository for such data. Here we present the
   web platform openSNP, an open database which allows participants of
   Direct-To-Consumer genetic testing to publish their genetic data at no
   cost along with phenotypic information. Through this crowdsourced effort
   of collecting genetic and phenotypic information, openSNP has become a
   resource for a wide area of studies, including Genome-Wide Association
   Studies. openSNP is hosted at http://www.opensnp.org, and the code is
   released under MIT-license at http://github.com/gedankenstuecke/snpr.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Greshake, B (Corresponding Author), Biodivers \& Climate Res Ctr, Mol Ecol Grp, Frankfurt, Germany.
   Greshake, Bastian, Biodivers \& Climate Res Ctr, Mol Ecol Grp, Frankfurt, Germany.
   Greshake, Bastian, Goethe Univ Frankfurt, Dept Appl Bioinformat, Inst Cell Biol \& Neurosci, D-60054 Frankfurt, Germany.
   Bayer, Philipp E., Univ Queensland, Sch Land Crop \& Food Sci, Brisbane, Qld, Australia.
   Bayer, Philipp E., Univ Queensland, Sch Agr \& Food Sci, Australian Ctr Plant Funct Genom, Brisbane, Qld, Australia.
   Rausch, Helge, Hsch Tech \& Wirtschaft, Berlin, Germany.
   Reda, Julia, Johannes Gutenberg Univ Mainz, D-55122 Mainz, Germany.},
DOI = {10.1371/journal.pone.0089204},
Article-Number = {e89204},
ISSN = {1932-6203},
Keywords-Plus = {DATABASE; CANCER; ISSUES},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {info@opensnp.org},
Affiliations = {Goethe University Frankfurt; University of Queensland; University of
   Queensland; Johannes Gutenberg University of Mainz},
ResearcherID-Numbers = {Greshake, Bastian/ABF-7171-2020
   Bayer, Philipp Emanuel/L-4481-2018},
ORCID-Numbers = {Greshake, Bastian/0000-0002-9925-9623
   Bayer, Philipp Emanuel/0000-0001-8530-3067},
Funding-Acknowledgement = {German Wikimedia Foundation},
Funding-Text = {The study was partially funded by 5000(sic) from the German Wikimedia
   Foundation (http://www.wikimedia.de/wiki/Hauptseite) in the context of
   their WissensWert contest, which funds projects for the use of open
   licenses to create a more open culture (2011)
   (http://de.wikipedia.org/wiki/Wikipedia:WissensWert). The funders had no
   role in study design, data collection and analysis, decision to publish,
   or preparation of the manuscript. No additional external funding was
   received for this study.},
Number-of-Cited-References = {42},
Times-Cited = {53},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {23},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {AD6ER},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000333348500004},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000762574000001,
Author = {Boone, Samuel C. and Dalton, Hayden and Prent, Alexander and Kohlmann,
   Fabian and Theile, Moritz and Greau, Yoann and Florin, Guillaume and
   Noble, Wayne and Hodgekiss, Sally-Ann and Ware, Bryant and Phillips,
   David and Kohn, Barry and O'Reilly, Suzanne and Gleadow, Andrew and
   McInnes, Brent and Rawling, Tim},
Title = {AusGeochem: An Open Platform for Geochemical Data Preservation,
   Dissemination and Synthesis},
Journal = {GEOSTANDARDS AND GEOANALYTICAL RESEARCH},
Year = {2022},
Volume = {46},
Number = {2},
Pages = {245-259},
Month = {JUN},
Abstract = {To promote a more efficient and transparent geochemistry data ecosystem,
   a consortium of Australian university research laboratories called the
   AuScope Geochemistry Network assembled to build a collaborative platform
   for the express purpose of preserving, disseminating and collating
   geochronology and isotopic data. In partnership with
   geoscience-data-solutions company Lithodat Pty Ltd, the open,
   cloud-based AusGeochem platform () was developed to simultaneously serve
   as a geosample registry, a geochemical data repository and a data
   analysis tool. Informed by method-specific groups of geochemistry
   experts and established international data reporting practices,
   community-agreed database schemas were developed for rock and mineral
   geosample metadata and secondary ion mass spectrometry U-Pb analysis,
   with additional models for laser ablation-inductively coupled-mass
   spectrometry U-Pb and Lu-Hf, Ar-Ar, fission-track and (U-Th-Sm)/He under
   development. Collectively, the AusGeochem platform provides the
   geochemistry community with a new, dynamic resource to help facilitate
   FAIR (Findable, Accessible, Interoperable, Reusable) data management,
   streamline data dissemination and advanced quantitative investigations
   of Earth system processes. By systematically archiving detailed
   geochemical (meta-)data in structured schemas, intractably large
   datasets comprising thousands of analyses produced by numerous
   laboratories can be readily interrogated in novel and powerful ways.
   These include rapid derivation of inter-data relationships, facilitating
   on-the-fly data compilation, analysis and visualisation.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Boone, SC (Corresponding Author), Univ Melbourne, Sch Geog Earth \& Atmospher Sci, Melbourne, Vic 3010, Australia.
   Boone, Samuel C.; Dalton, Hayden; Phillips, David; Kohn, Barry; Gleadow, Andrew, Univ Melbourne, Sch Geog Earth \& Atmospher Sci, Melbourne, Vic 3010, Australia.
   Prent, Alexander; Ware, Bryant; McInnes, Brent, Curtin Univ, John de Laeter Ctr, Bentley, WA 6102, Australia.
   Kohlmann, Fabian; Theile, Moritz; Noble, Wayne, Lithodat Pty Ltd, Melbourne, Vic 3030, Australia.
   Greau, Yoann; Florin, Guillaume; Hodgekiss, Sally-Ann; O'Reilly, Suzanne, Macquarie Univ, Dept Earth \& Environm Sci, Sydney, NSW 2109, Australia.
   Rawling, Tim, Univ Melbourne, AuScope, Melbourne, Vic 3010, Australia.},
DOI = {10.1111/ggr.12419},
EarlyAccessDate = {MAR 2022},
ISSN = {1639-4488},
EISSN = {1751-908X},
Keywords = {geochemical data platform; geosample registry; data repository; Big
   data; FAIR data},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {samuel.boone@unimelb.edu.au},
Affiliations = {University of Melbourne; Curtin University; Macquarie University;
   University of Melbourne},
ResearcherID-Numbers = {Gréau, Yoann/A-2885-2012
   Boone, Samuel C/AFC-9006-2022
   O'Reilly, Suzanne Y/A-1315-2008
   },
ORCID-Numbers = {Gréau, Yoann/0000-0002-8458-3746
   Boone, Samuel C/0000-0003-2274-7933
   O'Reilly, Suzanne Y/0000-0002-3883-5498
   Florin, Guillaume/0000-0002-1480-1162
   Prent, Alexander/0000-0002-1321-7319},
Funding-Acknowledgement = {AuScope program of the Australian National Collaborative Research
   Infrastructure Strategy (NCRIS)},
Funding-Text = {AusGeochem development is funded by the AuScope program of the
   Australian National Collaborative Research Infrastructure Strategy
   (NCRIS). The AuScope Geochemistry Network member research groups and
   laboratories would also like to acknowledge the significant support
   received over the last many decades from AuScope, the Australian
   Research Council and Australian Geodynamics Cooperative Research Centre
   for the procurement of analytical instrumentation and production of
   geochemical data. We would like to thank the Australian Research Data
   Commons, the International Geo Sample Number e.V. Executive Board,
   Jolyon Ralph of Mindat.org and the Expert Advisory Group members for
   their on-going support and assistance during the formation of the AGN
   and development of AusGeochem. We kindly thank Kathryn Linge, Lesley
   Wyborn and one anonymous reviewer for their thoughtful and constructive
   feedback. Open access publishing facilitated by The University of
   Melbourne, as part of the Wiley - The University of Melbourne agreement
   via the Council of Australian University Librarians.},
Number-of-Cited-References = {47},
Times-Cited = {7},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Geostand. Geoanal. Res.},
Doc-Delivery-Number = {1J0GX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000762574000001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000742498800001,
Author = {Kochueva, Olga and Nikolskii, Kirill},
Title = {Data Analysis and Symbolic Regression Models for Predicting CO and
   NO<sub>x</sub> Emissions from Gas Turbines},
Journal = {COMPUTATION},
Year = {2021},
Volume = {9},
Number = {12},
Month = {DEC},
Abstract = {Predictive emission monitoring systems (PEMS) are software solutions for
   the validation and supplementation of costly continuous emission
   monitoring systems for natural gas electrical generation turbines. The
   basis of PEMS is that of predictive models trained on past data to
   estimate emission components. The gas turbine process dataset from the
   University of California at Irvine open data repository has initiated a
   challenge of sorts to investigate the quality of models of various
   machine learning methods to build a model for predicting CO and NOx
   emissions depending on ambient variables and the parameters of the
   technological process. The novelty and features of this paper are: (i) a
   contribution to the study of the features of the open dataset on CO and
   NOx emissions for gas turbines, which will enable one to more
   objectively compare different machine learning methods for further
   research; (ii) for the first time for the CO and NOx emissions, a model
   based on symbolic regression and a genetic algorithm is presented-the
   advantage of this being the transparency of the influence of factors and
   the interpretability of the model; (iii) a new classification model
   based on the symbolic regression model and fuzzy inference system is
   proposed. The coefficients of determination of the developed models are:
   R-2=0.83 for NOx emissions, R-2=0.89 for CO emissions.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Kochueva, O (Corresponding Author), Natl Univ Oil \& Gas Gubkin Univ, Dept Appl Math \& Comp Modelling, 65 Leninsky Prospekt, Moscow 119991, Russia.
   Kochueva, Olga; Nikolskii, Kirill, Natl Univ Oil \& Gas Gubkin Univ, Dept Appl Math \& Comp Modelling, 65 Leninsky Prospekt, Moscow 119991, Russia.},
DOI = {10.3390/computation9120139},
Article-Number = {139},
EISSN = {2079-3197},
Keywords = {predictive emission monitoring systems; exhaust emissions prediction; CO
   emissions; NOx emissions; gas turbines; machine learning; symbolic
   regression; genetic algorithm; fuzzy classification model},
Research-Areas = {Mathematics},
Web-of-Science-Categories  = {Mathematics, Interdisciplinary Applications},
Author-Email = {olgakoch@mail.ru
   kochueva.o@gubkin.ru},
Affiliations = {Gubkin Russian State University of Oil \& Gas},
ResearcherID-Numbers = {Кочуева, Ольга/AAG-6100-2021},
ORCID-Numbers = {Кочуева, Ольга/0000-0002-7919-4746},
Number-of-Cited-References = {22},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Computation},
Doc-Delivery-Number = {YG4ZN},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000742498800001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000705525800002,
Author = {Pommier, C. and Michotey, C. and Cornut, G. and Roumet, P. and Duchene,
   E. and Flores, R. and Lebreton, A. and Alaux, M. and Durand, S. and
   Kimmel, E. and Letellier, T. and Merceron, G. and Laine, M. and Guerche,
   C. and Loaec, M. and Steinbach, D. and Laporte, M. A. and Arnaud, E. and
   Quesneville, H. and Adam-Blondon, A. F.},
Title = {Applying FAIR Principles to Plant Phenotypic Data Management in GnpIS},
Journal = {PLANT PHENOMICS},
Year = {2019},
Volume = {2019},
Abstract = {GnpIS is a data repository for plant phenomics that stores whole field
   and greenhouse experimental data including environment measures. It
   allows long-term access to datasets following the FAIR principles:
   Findable, Accessible, Interoperable, and Reusable, by using a flexible
   and original approach. It is based on a generic and ontology driven data
   model and an innovative software architecture that uncouples data
   integration, storage, and querying. It takes advantage of international
   standards including the Crop Ontology, MIAPPE, and the Breeding API.
   GnpIS allows handling data for a wide range of species and experiment
   types, including multiannual perennial plants experimental network or
   annual plant trials with either raw data, i.e., direct measures, or
   computed traits. It also ensures the integration and the
   interoperability among phenotyping datasets and with genotyping data.
   This is achieved through a careful curation and annotation of the key
   resources conducted in close collaboration with the communities
   providing data. Our repository follows the Open Science data publication
   principles by ensuring citability of each dataset. Finally, GnpIS
   compliance with international standards enables its interoperability
   with other data repositories hence allowing data links between phenotype
   and other data types. GnpIS can therefore contribute to emerging
   international federations of information systems.},
Publisher = {AMER ASSOC ADVANCEMENT SCIENCE},
Address = {1200 NEW YORK AVE, NW, WASHINGTON, DC 20005 USA},
Type = {Article},
Language = {English},
Affiliation = {Pommier, C (Corresponding Author), Univ Paris Saclay, INRA, URGI, F-78026 Versailles, France.
   Pommier, C.; Michotey, C.; Cornut, G.; Flores, R.; Lebreton, A.; Alaux, M.; Durand, S.; Kimmel, E.; Letellier, T.; Merceron, G.; Laine, M.; Guerche, C.; Loaec, M.; Steinbach, D.; Quesneville, H.; Adam-Blondon, A. F., Univ Paris Saclay, INRA, URGI, F-78026 Versailles, France.
   Roumet, P., Univ Montpellier, Montpellier SupAgro, INRA, CIRAD,AGAP, Montpellier, France.
   Duchene, E., UMR SVQV, 28 Rue Herrlisheim,BP 20507, F-68021 Colmar, France.
   Laporte, M. A.; Arnaud, E., Biovers Int, Parc Sci Agropolis 2, F-34397 Montpellier 5, France.},
DOI = {10.34133/2019/1671403},
Article-Number = {1671403},
ISSN = {2643-6515},
Research-Areas = {Agriculture; Plant Sciences; Remote Sensing},
Web-of-Science-Categories  = {Agronomy; Plant Sciences; Remote Sensing},
Author-Email = {cyril.pommier@inra.fr},
Affiliations = {INRAE; Universite Paris Saclay; INRAE; Institut Agro; Montpellier
   SupAgro; Universite de Montpellier; CIRAD; Alliance; Bioversity
   International},
ORCID-Numbers = {Roumet, Pierre/0000-0003-1054-2156
   Alaux, Michael/0000-0001-9356-4072
   Pommier, Cyril/0000-0002-9040-8733
   Laporte, Marie-Angelique/0000-0002-8461-9745
   Michotey, Celia/0000-0003-1877-1703},
Funding-Acknowledgement = {INRA; Infrastructure Biologie Sante `Phenome-FPPN' - French National
   Research Agency {[}ANR-11-INBS-0012]; TransPLANT project (EU 7th
   Framework Program) {[}283496]; H2020 ELIXIR-EXCELERATE project (European
   Commission within the Research Infrastructures programme of Horizon
   2020) {[}676559]; ``Investments for the Future programme{''} (PIA)
   {[}ANR-11-INBS-0012]; Breedwheat PIA project {[}ANR-10-BTBR03]; BFF PIA
   project {[}11-BTBR-0006]; Rapsodyn PIA project {[}11-BTBR-0004]; Peamust
   PIA project {[}11-BTBR-0002]; RDA Europe Project - European Commission},
Funding-Text = {We gratefully acknowledge the whole INRA Ephesis User Committee for
   inputs and help in specifying GnpIS-Ephesis functionalities: P. Bertin,
   A. Charcosset, C. Lecomte, A. Klein, A. Raffin, B. Quillot, P. Burger,
   E. Costes, A. Dimouro, C. Pichot, J.B. Magnin-Robert, J. Quero-Garcia,
   E. Balsemin, and A. Gauffreteau. We thank C. Anger and the whole French
   Common Garden network (Plantacomp) for their contribution to the
   specifications and data publication. We are grateful to the other
   members of the Phenome-Emphasis.fr information system team, including V.
   Negre, A. Tireau, and in particular P. Neveu, for continuous fruitful
   discussions. We are grateful to the Straw CerealNetwork leaders, G.
   Charmet, F.X. Oury, and A. Gauffreteau, who entrusted GnpIS for the
   publication of their data that made the first important public use case.
   We thank our datamanager teamfor their contribution in data integration:
   D. Charruaud, M. Labernardi`ere, S. Diagne, N. Mohellibi, and in
   particular N. Francillonne and more generally the INRAURGI platformfor
   themaintenance of GnpIS. We also thank the Crop ontology Community,
   including L. Valette as well as R. Shrestha of the CIMMYT; the MIAPPE
   community, especially P. Kersey, P. Krajewsky, and H. Cwiek. We are also
   grateful to the BrAPI community and especially to L. Mueller, J.E.
   Backlund, and P. Selby for their collaborative initiatives and
   continuous productive discussions. We also thank the INRA Gitlab team
   and especially Damien Berry, Maurice Baudry, and Christian Poirier for
   the FORGE MIA service. We have reused in the figures the images provided
   by INRA (JeanWeber (c) INRA and Raphael Segura (c) INRA). This work was
   supported by INRA, by the Infrastructure Biologie Sant ` e
   `Phenome-FPPN' supported by the French National Research Agency
   (ANR-11-INBS-0012), the TransPLANT project (EU 7th Framework Program,
   Contract no. 283496), the H2020 ELIXIR-EXCELERATE project (funded by the
   European Commission within the Research Infrastructures programme of
   Horizon 2020, Grant agreement no. 676559), and the ``Investments for the
   Future programme{''} (PIA) (ANR-11-INBS-0012). Developments of Wheat,
   protein crops, rapeseed, and miscanthus ontologies have been supported
   by the Breedwheat (ANR-10-BTBR03), BFF (11-BTBR-0006), Rapsodyn
   (11-BTBR-0004), and Peamust (11-BTBR-0002) PIA projects. In-kind
   contribution was made by the Crop Ontology project team supported by the
   Integrated Breeding Platform and by the CGIAR Platform on Big Data for
   Agriculture. Some developments were supported by the RDA Europe Project
   funded by the European Commission.},
Number-of-Cited-References = {40},
Times-Cited = {27},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {18},
Journal-ISO = {Plant Phenomics},
Doc-Delivery-Number = {VK4YR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000705525800002},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000368296000017,
Author = {Garcia-Garcia, Alicia and Lopez-Borrull, Alexandre and Peset, Fernanda},
Title = {Data journals: emergence of new journals specializing in data},
Journal = {PROFESIONAL DE LA INFORMACION},
Year = {2015},
Volume = {24},
Number = {6},
Pages = {845-854},
Month = {NOV-DEC},
Abstract = {Two major facts: the huge increase in the amount of data that scientists
   produce, and the pressure for transparency and economic efficiency of
   public budgets, have caused that a good data management has become much
   more important. A compilation and an analysis of some data journals -
   journals specializing in data- is presented. Their origins, evolution
   and characteristics are described. Finally, a reflection is done on the
   role that data journals can play in the scientific communication
   ecosystem.},
Publisher = {EPI},
Address = {APARTADO 32 280, BARCELONA, 08080, SPAIN},
Type = {Article},
Language = {Spanish},
Affiliation = {García-García, A (Corresponding Author), Univ Politecn Valencia, Proyecto Datasea, Camino Vera S-N, E-46022 Valencia, Spain.
   Garcia-Garcia, Alicia, Univ Politecn Valencia, Proyecto Datasea, E-46022 Valencia, Spain.
   Lopez-Borrull, Alexandre, Univ Oberta Catalunya, Estudis Informacio \& Comunicacio, Barcelona 08018, Spain.
   Peset, Fernanda, Univ Politecn Valencia, Dept Comunicac Audiovisual Documentac \& Hist Arte, E-46022 Valencia, Spain.},
DOI = {10.3145/epi.2015.nov.17},
ISSN = {1386-6710},
Keywords = {Data journals; Data papers; Data repositories; Data publication;
   Scientific publishing; Open data; Peer review},
Keywords-Plus = {MODELS},
Research-Areas = {Communication; Information Science \& Library Science},
Web-of-Science-Categories  = {Communication; Information Science \& Library Science},
Author-Email = {alimore17@gmail.com
   alopezbo@uoc.edu
   mpesetm@upv.es},
Affiliations = {Universitat Politecnica de Valencia; UOC Universitat Oberta de
   Catalunya; Universitat Politecnica de Valencia},
ResearcherID-Numbers = {López-Borrull, Alexandre/C-4363-2013
   PESET, FERNANDA/A-8491-2008
   Garcia-Garcia, Alicia/AAA-5177-2019
   },
ORCID-Numbers = {López-Borrull, Alexandre/0000-0003-1609-2088
   Garcia-Garcia, Alicia/0000-0003-3597-3964
   Peset, Fernanda/0000-0003-3706-6532},
Number-of-Cited-References = {29},
Times-Cited = {11},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {33},
Journal-ISO = {Prof. Inf.},
Doc-Delivery-Number = {DB1VB},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000368296000017},
OA = {Green Submitted, Green Published, Bronze, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000439733400012,
Author = {Ondei, Stefania and Brook, Barry W. and Buettel, Jessie C.},
Title = {Nature's untold stories: an overview on the availability and type of
   on-line data on long-term biodiversity monitoring},
Journal = {BIODIVERSITY AND CONSERVATION},
Year = {2018},
Volume = {27},
Number = {11},
Pages = {2971-2987},
Month = {SEP},
Abstract = {Long-term field-based monitoring is time and resource demanding.
   Consequently, there are few robust biodiversity databases that contain
   both a baseline and repeat measurements. On-line repositories represent
   a potential goldmine of conservation-relevant data, and are increasingly
   incentivized by funding agencies. However, there remains scarce
   information on their distribution and availability, limiting the
   possibility to exploit them to their full potential. Here we
   comprehensively searched and assessed open-access datasets where
   biodiversity has been monitored in the same site for at least 4 years,
   and where species and site locations were clearly reported. We located
   data on 75,669 field sites (9436 of which are in biodiversity hotspots),
   for a total of 28,723,226 records, monitoring a total of 15,046
   different taxa. We found strong geographic and taxonomic biases.
   Monitoring sites were predominantly located in the Palearctic and
   Nearctic biogeographic realms and in the forest biome. Where fauna was
   monitored, the focus was mostly on amphibians and birds. Supporting
   open-access policies and developing strategies to fill the identified
   gaps will be crucial for improving our understanding of global
   biodiversity trends. Our results suggest, however, that we are on the
   right trajectory, with a vast storehouse of readily available (and often
   high quality) yet largely under-analysed biodiversity data now available
   online from a range of sources. We argue that such data can provide the
   required biodiversity baselines for national- or local-scale studies.},
Publisher = {SPRINGER},
Address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Ondei, S (Corresponding Author), Univ Tasmania, Sch Nat Sci, Sandy Bay, Tas, Australia.
   Ondei, Stefania; Brook, Barry W.; Buettel, Jessie C., Univ Tasmania, Sch Nat Sci, Sandy Bay, Tas, Australia.
   Brook, Barry W.; Buettel, Jessie C., Univ Tasmania, ARC Ctr Excellence Australian Biodivers \& Heritag, Hobart, Tas, Australia.},
DOI = {10.1007/s10531-018-1582-2},
ISSN = {0960-3115},
EISSN = {1572-9710},
Keywords = {Biodiversity; Long-term ecological research; Ecosystem monitoring
   networks; Data repositories; Biomes; Biogeographic realms},
Keywords-Plus = {PLANT DIVERSITY; ECOREGIONS; OPPORTUNITIES; REPTILES; ECOLOGY; SCIENCE;
   WORLD; LIFE; MAP},
Research-Areas = {Biodiversity \& Conservation; Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Biodiversity Conservation; Ecology; Environmental Sciences},
Author-Email = {stefania.ondei@utas.edu.au},
Affiliations = {University of Tasmania; University of Tasmania},
ResearcherID-Numbers = {CABAH, ARC/T-6419-2019
   Ondei, Stefania/AAL-4091-2020
   Brook, Barry/G-2686-2011
   },
ORCID-Numbers = {Ondei, Stefania/0000-0002-2515-3316
   Brook, Barry/0000-0002-2491-1517
   Buettel, Jessie/0000-0001-6737-7468},
Funding-Acknowledgement = {Australian Research Council Laureate Fellowship {[}FL160100101]},
Funding-Text = {This study was supported by Australian Research Council Laureate
   Fellowship under Award Number FL160100101.},
Number-of-Cited-References = {67},
Times-Cited = {11},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {28},
Journal-ISO = {Biodivers. Conserv.},
Doc-Delivery-Number = {GO1RV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000439733400012},
DA = {2024-01-15},
}

@article{ WOS:000691823600004,
Author = {Descoteaux, Danielle and Farinelli, Chiara and Soares e Silva, Marina
   and de Waard, Anita},
Title = {Playing Well on the Data FAIRground: Initiatives and Infrastructure in
   Research Data Management},
Journal = {DATA INTELLIGENCE},
Year = {2019},
Volume = {1},
Number = {4},
Pages = {350-367},
Month = {FAL},
Abstract = {Over the past five years, Elsevier has focused on implementing FAIR and
   best practices in data management, from data preservation through reuse.
   In this paper we describe a series of efforts undertaken in this time to
   support proper data management practices. In particular, we discuss our
   journal data policies and their implementation, the current status and
   future goals for the research data management platform Mendeley Data,
   and clear and persistent linkages to individual data sets stored on
   external data repositories from corresponding published papers through
   partnership with Scholix. Early analysis of our data policies
   implementation confirms significant disparities at the subject level
   regarding data sharing practices, with most uptake within disciplines of
   Physical Sciences. Future directions at Elsevier include implementing
   better discoverability of linked data within an article and
   incorporating research data usage metrics.},
Publisher = {MIT PRESS},
Address = {ONE ROGERS ST, CAMBRIDGE, MA 02142-1209 USA},
Type = {Article},
Language = {English},
Affiliation = {Descoteaux, D (Corresponding Author), Elsevier Inc, 50 Hampshire St, Cambridge, MA 02139 USA.
   Descoteaux, Danielle; de Waard, Anita, Elsevier Inc, 50 Hampshire St, Cambridge, MA 02139 USA.
   Farinelli, Chiara; Soares e Silva, Marina, Elsevier BV, Radarweg 29, NL-2043 NX Amsterdam, Netherlands.},
DOI = {10.1162/dint\_a\_00020},
EISSN = {2641-435X},
Keywords = {Open data; Data sharing; Data citation; Open research},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Author-Email = {d.descoteaux@elsevier.com
   c.fennell@elsevier.com
   m.soaresesilva@elsevier.com
   A.dewaard@elsevier.com},
Affiliations = {Reed Elsevier; Elsevier; Reed Elsevier; Elsevier},
ORCID-Numbers = {Farinelli, Chiara/0000-0001-5698-4705},
Number-of-Cited-References = {18},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Data Intell.},
Doc-Delivery-Number = {VK4BE},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000691823600004},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000838145400001,
Author = {Boschert, Claire and Dikow, Torsten},
Title = {Taxonomic revision of the mydas-fly genera <i>Eremohaplomydas</i>
   Bequaert, 1959, <i>Haplomydas</i> Bezzi, 1924, and <i>Lachnocorynus</i>
   Hesse, 1969 (Insecta, Diptera, Mydidae)},
Journal = {AFRICAN INVERTEBRATES},
Year = {2022},
Volume = {63},
Number = {1},
Pages = {19-75},
Month = {MAR 25},
Abstract = {The genera Eremohaplomydas Bequaert, 1959, Haplomydas Bezzi, 1924, and
   Lachnocorynus Hesse, 1969 (Diptera: Mydidae: Syllegomydinae) are
   revised. Currently, four species are known from southern Africa, i.e.,
   Eremohaplomydas desertorum Bequaert, 1959 from north-western Namibia,
   Haplomydas crassipes Bezzi, 1924 widespread in southern Africa,
   Lachnocorynus chobeensis Hesse, 1969 from northern Botswana, and
   Lachnocorynus kochi Hesse, 1969 from northern Namibia. Four new species,
   Eremohaplomydas gobabebensis sp. nov. and Eremohaplomydas whartoni sp.
   nov. from the central Namib desert of Namibia, Eremohaplomydas
   stomachoris sp. nov. from the northern Namib desert in Namibia, and
   Lachnocorynus stenocephalus sp. nov. from north-eastern Zimbabwe are
   described. Lachnocorynus kochi is synonymized with Lachnocorynus
   chobeensis. Distribution, biology, occurrence in biodiversity hotspots
   sensu Conservation International and seasonal imago flight activity are
   discussed. Descriptions/redescriptions, photographs, specimen occurrence
   data, and identification keys (both dichotomous and matrix-based) to
   species are provided and made openly accessible in data repositories to
   support and accelerate future studies of the included taxa. An updated
   identification key to the Mydidae genera of the Afrotropical Region is
   provided. The placement of the three genera in the subfamily taxon
   Syllegomydinae is discussed and several morphological features, such as
   an extremely reduced proboscis in some species, a unique wing venation
   in Eremohaplomydas gobabebensis sp. nov., and the unique metathoracic
   coxa, are discussed.},
Publisher = {COUNCIL NATAL MUSEUM},
Address = {PRIVATE BAG 9070, PIETERMARITZBURG, KWAZULU-NATAL 00000, SOUTH AFRICA},
Type = {Article},
Language = {English},
Affiliation = {Dikow, T (Corresponding Author), Smithsonian Inst, Natl Museum Nat Hist, Dept Entomol, 10th St \& Constitut Ave NW, Washington, DC 20560 USA.
   Boschert, Claire, Rice Univ, Houston, TX USA.
   Dikow, Torsten, Smithsonian Inst, Natl Museum Nat Hist, Dept Entomol, 10th St \& Constitut Ave NW, Washington, DC 20560 USA.},
DOI = {10.3897/AfrInvertebr.63.76309},
ISSN = {1681-5556},
EISSN = {2305-2562},
Keywords = {Afrotropical; cybertaxonomy; Karoo; Mydas flies; Namib Desert;
   open-access},
Research-Areas = {Entomology; Paleontology; Zoology},
Web-of-Science-Categories  = {Entomology; Paleontology; Zoology},
Author-Email = {DikowT@si.edu},
Affiliations = {Rice University; Smithsonian Institution; Smithsonian National Museum of
   Natural History},
ResearcherID-Numbers = {Dikow, Torsten/H-3103-2019},
ORCID-Numbers = {Dikow, Torsten/0000-0003-4816-2909},
Funding-Acknowledgement = {U.S. National Science Foundation (NSF) {[}OCE 1560088]},
Funding-Text = {We would like to thank the many museum curators for making specimens
   available through loans and for their hospitality when visiting the
   collections. We would also like to graciously acknowledge the U.S.
   National Science Foundation (NSF) for funding the Research Experience
   for Undergraduates site grant at the NMNH entitled ``Natural History
   Research Experience (NHRE){''} (OCE 1560088; PI E. Cottrell, CoPI E.
   Hunt). We thank Virginia Power, Liz Cottrell, and Gene Hunt for their
   constant support during the administration of the NHRE programme. We
   also acknowledge field work support to the junior author from the NMNH
   for a project entitled, ``Novel morphological data to decipher the
   character and life history evolution and diversification of Asiloidea
   and Nemestrinoidea flies{''} (2017). John Hash (formerly NMNH) is
   thanked for taking the photographs of proboscides and Gillian
   MaggsKolling (Gobabeb Namib Research Institute) is thanked for help in
   identifying the grasses in Figs 1-2. We thank Marcus Guidoti and Donat
   Agosti (both Plazi) for developing the image repository at the Zenodo
   Biodiversity Literature Repository and help with uploading the image
   files. Furthermore, we thank the Namibian National Commission on
   Research, Science and Technology (NCRST) and the Ministry of Environment
   and Tourism (MET) for providing collecting and export permits in support
   of the field work in Namibia. The junior author would like to thank
   Charlotte Alberts (UC Davis), Allan Cabrero (UC Berkeley), and Brandon
   Claridge (Utah State University) for accompanying him in the field in
   Namibia and Gillian Maggs Kolling, Leena Kapulwa, and Eugene Marais
   (Gobabeb Namib Research Institute) for all the support prior and during
   our stay at the station. Lastly, we thank Jason Londt and an anonymous
   reviewer for their constructive comments during peer review.},
Number-of-Cited-References = {26},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Afr. Invertebr.},
Doc-Delivery-Number = {3Q3PB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000838145400001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000563240000001,
Author = {Ueckermann, Mattheus P. and Bieszczad, Jerry and Entekhabi, Dara and
   Shapiro, Marc L. and Callendar, David R. and Sullivan, David and Milloy,
   Jeffrey},
Title = {PODPAC: open-source Python software for enabling harmonized,
   plug-and-play processing of disparate earth observation data sets and
   seamless transition onto the serverless cloud by earth scientists},
Journal = {EARTH SCIENCE INFORMATICS},
Year = {2020},
Volume = {13},
Number = {4},
Pages = {1507-1521},
Month = {DEC},
Abstract = {In this paper, we present the Pipeline for Observational Data
   Processing, Analysis, and Collaboration (PODPAC) software. PODPAC is an
   open-source Python library designed to enable widespread exploitation of
   NASA earth science data by enabling multi-scale and multi-windowed
   access, exploration, and integration of available earth science datasets
   to support analysis and analytics; automatic accounting for geospatial
   data formats, projections, and resolutions; simplified implementation
   and parallelization of geospatial data processing routines; standardized
   sharing of data and algorithms; and seamless transition of algorithms
   and data products from local development to distributed, serverless
   processing on commercial cloud computing environments. We describe the
   key elements of PODPAC's architecture, includingNodesfor unified
   encapsulation of disparate scientific data sources;Algorithmsfor
   plug-and-play processing and harmonization of multiple data sourceNodes;
   andLambda functionsfor serverless execution and sharing of new data
   products via the cloud. We provide an overview of our open-source code
   implementation and testing process for development and deployment of
   PODPAC. We describe our interactive, JupyterLab-based end-user
   documentation including quick-start examples and detailed use case
   studies. We conclude with examples of PODPAC's application to:
   encapsulate data sources available on Amazon Web Services (AWS) Open
   Data repository; harmonize processing of multiple earth science data
   sets for downscaling of NASA Soil Moisture Active Passive (SMAP) soil
   moisture data; and deploy a serverless SMAP-based drought monitoring
   application for use access from mobile devices. We postulate that PODPAC
   will also be an effective tool for wrangling and standardizing massive
   earth science data sets for use in model training for machine learning
   applications.},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Ueckermann, MP (Corresponding Author), Creare LLC, Hanover, NH 03755 USA.
   Ueckermann, Mattheus P.; Bieszczad, Jerry; Shapiro, Marc L.; Callendar, David R.; Sullivan, David; Milloy, Jeffrey, Creare LLC, Hanover, NH 03755 USA.
   Entekhabi, Dara, MIT, 77 Massachusetts Ave, Cambridge, MA 02139 USA.},
DOI = {10.1007/s12145-020-00506-0},
EarlyAccessDate = {AUG 2020},
ISSN = {1865-0473},
EISSN = {1865-0481},
Keywords = {Data harmonization; Plug-and-play algorithms; Reproducibility;
   Serverless cloud computing; Python; JupyterLab; SMAP},
Research-Areas = {Computer Science; Geology},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Geosciences,
   Multidisciplinary},
Author-Email = {mpu@creare.com},
Affiliations = {Creare Research \& Development, Inc.; Massachusetts Institute of
   Technology (MIT)},
ORCID-Numbers = {Ueckermann, Mattheus/0000-0003-3615-4610},
Funding-Acknowledgement = {NASA under SBIR Phase II {[}80NSSC18C0061]},
Funding-Text = {This research is supported by NASA under SBIR Phase II Contract No.
   80NSSC18C0061. We gratefully acknowledge the developers of the open
   source software libraries on which PODPAC depends, in particular
   Anaconda, GDAL, JupyterLab, numpy, proj4J, rasterio, scipy and xarray.
   The SMAP data used in this study can be downloaded from
   https://nsidc.org/data/smap/smap-data.html.The global digital elevation
   model (DEM) data used in this study can be downloaded from
   http://viewfinderpanoramas.org/dem3.html.The TWI data used in this study
   can be downloaded viaWCS from https://mobility.crearecomputing.com/ogc?},
Number-of-Cited-References = {8},
Times-Cited = {0},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Earth Sci. Inform.},
Doc-Delivery-Number = {OT0JM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000563240000001},
DA = {2024-01-15},
}

@article{ WOS:000668260300001,
Author = {Takeuchi, Kosuke and Kunimoto, Ryo and Bajorath, Juergen},
Title = {R-group replacement database for medicinal chemistry},
Journal = {FUTURE SCIENCE OA},
Year = {2021},
Volume = {7},
Number = {8},
Month = {SEP},
Abstract = {Aim: Generation of an R-group replacement system for compound
   optimization in medicinal chemistry. Materials \& methods: From
   bioactive compounds, analogue series (ASs) were systematically extracted
   and from these ASs, all R-groups were isolated and further analyzed.
   Exemplary results \& data: From more than 17,000 ASs, more than 50,000
   unique R-groups were isolated. For the 500 most frequently used
   R-groups, preferred replacements were identified and organized in
   hierarchies. All original data and an R-group replacement database are
   made available in an open access deposition. Limitations \& next steps:
   The searchable database has no limitations and can easily be modified
   using the source data we provide. The next step will be applying this
   R-group resource in practical medicinal chemistry projects as decision
   support.},
Publisher = {FUTURE SCI LTD},
Address = {UNITED HOUSE, 2 ALBERT PL, LONDON, N3 1QB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bajorath, J (Corresponding Author), Rhein Friedrich Wilhelm Univ, Dept Life Sci Informat, B IT, LIMES Program Unit Chem Biol \& Med Chem, Friedrich Hirzebruch Allee 6, D-53113 Bonn, Germany.
   Takeuchi, Kosuke; Kunimoto, Ryo; Bajorath, Juergen, Rhein Friedrich Wilhelm Univ, Dept Life Sci Informat, B IT, LIMES Program Unit Chem Biol \& Med Chem, Friedrich Hirzebruch Allee 6, D-53113 Bonn, Germany.},
DOI = {10.2144/fsoa-2021-0062},
EarlyAccessDate = {JUN 2021},
Article-Number = {FSO742},
ISSN = {2056-5623},
Keywords = {analogue series; compound optimization; data repository; network data
   structure; replacements; R-groups},
Research-Areas = {Research \& Experimental Medicine},
Web-of-Science-Categories  = {Medicine, Research \& Experimental},
Author-Email = {bajorath@bit.uni-bonn.de},
Affiliations = {University of Bonn},
ORCID-Numbers = {Kunimoto, Ryo/0000-0003-4895-9686
   Bajorath, Jurgen/0000-0002-0557-5714},
Number-of-Cited-References = {17},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Futur. Sci. OA},
Doc-Delivery-Number = {TK2EM},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000668260300001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000853433600001,
Author = {Jones, Andrew R. and Deutsch, Eric W. and Vizcaino, Juan Antonio},
Title = {Is DIA proteomics data FAIR? Current data sharing practices, available
   bioinformatics infrastructure and recommendations for the future},
Journal = {PROTEOMICS},
Year = {2023},
Volume = {23},
Number = {7-8, SI},
Month = {APR},
Abstract = {Data independent acquisition (DIA) proteomics techniques have matured
   enormously in recent years, thanks to multiple technical developments
   in, for example, instrumentation and data analysis approaches. However,
   there are many improvements that are still possible for DIA data in the
   area of the FAIR (Findability, Accessibility, Interoperability and
   Reusability) data principles. These include more tailored data sharing
   practices and open data standards since public databases and data
   standards for proteomics were mostly designed with DDA data in mind.
   Here we first describe the current state of the art in the context of
   FAIR data for proteomics in general, and for DIA approaches in
   particular. For improving the current situation for DIA data, we make
   the following recommendations for the future: (i) development of an open
   data standard for spectral libraries; (ii) make mandatory the
   availability of the spectral libraries used in DIA experiments in
   ProteomeXchange resources; (iii) improve the support for DIA data in the
   data standards developed by the Proteomics Standards Initiative; and
   (iv) improve the support for DIA datasets in ProteomeXchange resources,
   including more tailored metadata requirements.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Vizcaíno, JA (Corresponding Author), EMBL European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Cambridge CB10 1SD, England.
   Jones, Andrew R., Univ Liverpool, Inst Syst Mol \& Integrat Biol, Liverpool, Merseyside, England.
   Deutsch, Eric W., Inst Syst Biol, Washington, DC USA.
   Vizcaino, Juan Antonio, EMBL European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Cambridge CB10 1SD, England.},
DOI = {10.1002/pmic.202200014},
EarlyAccessDate = {SEP 2022},
Article-Number = {e2200014},
ISSN = {1615-9853},
EISSN = {1615-9861},
Keywords = {data independent acquisition; data repositories; data standards;
   proteomics data; spectral libraries},
Keywords-Plus = {MASS-SPECTROMETRY; REPRESENTATION; BENCHMARKING; EXPRESSION; STANDARD;
   LIBRARY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
Author-Email = {juan@ebi.ac.uk},
Affiliations = {University of Liverpool; Institute for Systems Biology (ISB); European
   Molecular Biology Laboratory (EMBL)},
ResearcherID-Numbers = {Deutsch, Eric/AAF-5912-2020
   Vizcaino, Juan Antonio/C-3691-2009},
ORCID-Numbers = {Vizcaino, Juan Antonio/0000-0002-3905-4335},
Funding-Acknowledgement = {Wellcome Trust {[}223745/Z/21/Z]; National Institutes of Health
   {[}R01GM087221, R24GM127667, U19AG023122]; European Commission
   {[}823839]; Biotechnology and Biological Sciences Research Council
   {[}BB/P024599/1, BB/T019557/1, BB/T019670/1]; National Science
   Foundation {[}DBI-1933311, IOS-1922871]; Wellcome Trust
   {[}223745/Z/21/Z] Funding Source: Wellcome Trust},
Funding-Text = {Wellcome Trust, Grant/Award Number: 223745/Z/21/Z; National Institutes
   of Health, Grant/Award Numbers: R01GM087221, R24GM127667, U19AG023122;
   European Commission, Grant/Award Number: 823839; Biotechnology and
   Biological Sciences Research Council, Grant/Award Numbers: BB/P024599/1,
   BB/T019557/1, BB/T019670/1; National Science Foundation, Grant/Award
   Numbers: DBI-1933311, IOS-1922871},
Number-of-Cited-References = {41},
Times-Cited = {3},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Proteomics},
Doc-Delivery-Number = {D5BP9},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000853433600001},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000374649900001,
Author = {Arend, Daniel and Junker, Astrid and Scholz, Uwe and Schueler, Danuta
   and Wylie, Juliane and Lange, Matthias},
Title = {PGP repository: a plant phenomics and genomics data publication
   infrastructure},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2016},
Month = {APR 17},
Abstract = {Plant genomics and phenomics represents the most promising tools for
   accelerating yield gains and overcoming emerging crop productivity
   bottlenecks. However, accessing this wealth of plant diversity requires
   the characterization of this material using state-of-the-art genomic,
   phenomic and molecular technologies and the release of subsequent
   research data via a long-term stable, open-access portal. Although
   several international consortia and public resource centres offer
   services for plant research data management, valuable digital assets
   remains unpublished and thus inaccessible to the scientific community.
   Recently, the Leibniz Institute of Plant Genetics and Crop Plant
   Research and the German Plant Phenotyping Network have jointly initiated
   the Plant Genomics and Phenomics Research Data Repository (PGP) as
   infrastructure to comprehensively publish plant research data. This
   covers in particular cross-domain datasets that are not being published
   in central repositories because of its volume or unsupported data scope,
   like image collections from plant phenotyping and microscopy, unfinished
   genomes, genotyping data, visualizations of morphological plant models,
   data from mass spectrometry as well as software and documents.
   The repository is hosted at Leibniz Institute of Plant Genetics and Crop
   Plant Research using e!DAL as software infrastructure and a Hierarchical
   Storage Management System as data archival backend. A novel developed
   data submission tool was made available for the consortium that features
   a high level of automation to lower the barriers of data publication.
   After an internal review process, data are published as citable digital
   object identifiers and a core set of technical metadata is registered at
   DataCite. The used e!DAL-embedded Web frontend generates for each
   dataset a landing page and supports an interactive exploration. PGP is
   registered as research data repository at BioSharing.org, re3data.org
   and OpenAIRE as valid EU Horizon 2020 open data archive. Above features,
   the programmatic interface and the support of standard metadata formats,
   enable PGP to fulfil the FAIR data principles-findable, accessible,
   interoperable, reusable.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Arend, D (Corresponding Author), OT Gatersleben, Leibniz Inst Plant Genet \& Crop Plant Res IPK, Corrensstr 3, D-06466 Gatersleben, Germany.
   Arend, Daniel; Junker, Astrid; Scholz, Uwe; Schueler, Danuta; Wylie, Juliane; Lange, Matthias, OT Gatersleben, Leibniz Inst Plant Genet \& Crop Plant Res IPK, Corrensstr 3, D-06466 Gatersleben, Germany.},
DOI = {10.1093/database/baw033},
Article-Number = {baw033},
ISSN = {1758-0463},
Keywords-Plus = {CITATION; SCIENCE},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {arendd@ipk-gatersleben.de},
Affiliations = {Leibniz Institut fur Pflanzengenetik und Kulturpflanzenforschung},
ResearcherID-Numbers = {Scholz, Uwe/JWA-1330-2024
   },
ORCID-Numbers = {Arend, Daniel/0000-0002-2455-5938
   Scholz, Uwe/0000-0001-6113-3518
   Lange, Matthias/0000-0002-4316-078X
   Schuler, Danuta/0000-0003-4277-9879
   Junker, Astrid/0000-0002-4656-0308},
Funding-Acknowledgement = {German Federal Ministry of Education and Research {[}FKZ031A053];
   Leibniz Association, Chausseestrasse, Berlin, Germany},
Funding-Text = {Part of this work was performed within the German-Plant-Phenotyping
   Network, which is funded by the German Federal Ministry of Education and
   Research (project identification number: FKZ031A053). Funding for open
   access charge: Leibniz Association, Chausseestrasse 111, 10115 Berlin,
   Germany.},
Number-of-Cited-References = {30},
Times-Cited = {60},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {43},
Journal-ISO = {Database},
Doc-Delivery-Number = {DK1CK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000374649900001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000647649700008,
Author = {Manzano, Saul and Julier, Adele C. M.},
Title = {How FAIR are plant sciences in the twenty-first century? The pressing
   need for reproducibility in plant ecology and evolution},
Journal = {PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
Year = {2021},
Volume = {288},
Number = {1944},
Month = {FEB 10},
Abstract = {The need for open, reproducible science is of growing concern in the
   twenty-first century, with multiple initiatives like the widely
   supported FAIR principles advocating for data to be Findable,
   Accessible, Interoperable and Reusable. Plant ecological and
   evolutionary studies are not exempt from the need to ensure that the
   data upon which their findings are based are accessible and allow for
   replication in accordance with the FAIR principles. However, it is
   common that the collection and curation of herbarium specimens, a
   foundational aspect of studies involving plants, is neglected by
   authors. Without publicly available specimens, huge numbers of studies
   that rely on the field identification of plants are fundamentally not
   reproducible. We argue that the collection and public availability of
   herbarium specimens is not only good botanical practice but is also
   fundamental in ensuring that plant ecological and evolutionary studies
   are replicable, and thus scientifically sound. Data repositories that
   adhere to the FAIR principles must make sure that the original data are
   traceable to and re-examinable at their empirical source. In order to
   secure replicability, and adherence to the FAIR principles, substantial
   changes need to be brought about to restore the practice of collecting
   and curating specimens, to educate students of their importance, and to
   properly fund the herbaria which house them.},
Publisher = {ROYAL SOC},
Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Manzano, S (Corresponding Author), Univ Cape Town, Dept Biol Sci, Plant Conservat Unit, HW Pearson Bldg,Private Bag X3, ZA-7701 Rondebosch, South Africa.
   Manzano, Saul; Julier, Adele C. M., Univ Cape Town, Dept Biol Sci, Plant Conservat Unit, HW Pearson Bldg,Private Bag X3, ZA-7701 Rondebosch, South Africa.},
DOI = {10.1098/rspb.2020.2597},
Article-Number = {20202597},
ISSN = {0962-8452},
EISSN = {1471-2954},
Keywords = {FAIR principles; plant ecology; plant evolution; diversity;
   reproducibility; open science},
Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Environmental Sciences \&
   Ecology; Evolutionary Biology},
Web-of-Science-Categories  = {Biology; Ecology; Evolutionary Biology},
Author-Email = {saul.manzano.rodriguez@gmail.com},
Affiliations = {University of Cape Town},
ResearcherID-Numbers = {Julier, Adele/ABA-4833-2020
   Manzano, Saúl/ABB-6578-2021
   },
ORCID-Numbers = {Julier, Adele/0000-0003-1106-6008
   Manzano, Saul/0000-0002-5720-2768},
Funding-Acknowledgement = {NRF Competitive Programme for Rated Researchers {[}118538]; NRF African
   Origins Platform {[}117666]},
Funding-Text = {S.M. acknowledges funding from the NRF Competitive Programme for Rated
   Researchers (118538). A.C.M.J. acknowledges funding from the NRF African
   Origins Platform (117666).},
Number-of-Cited-References = {16},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Proc. R. Soc. B-Biol. Sci.},
Doc-Delivery-Number = {RY1AR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000647649700008},
OA = {Bronze, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000352160600027,
Author = {Siebert, S. and Kummu, M. and Porkka, M. and Doell, P. and Ramankutty,
   N. and Scanlon, B. R.},
Title = {A global data set of the extent of irrigated land from 1900 to 2005},
Journal = {HYDROLOGY AND EARTH SYSTEM SCIENCES},
Year = {2015},
Volume = {19},
Number = {3},
Pages = {1521-1545},
Abstract = {Irrigation intensifies land use by increasing crop yield but also
   impacts water resources. It affects water and energy balances and
   consequently the microclimate in irrigated regions. Therefore, knowledge
   of the extent of irrigated land is important for hydrological and crop
   modelling, global change research, and assessments of resource use and
   management. Information on the historical evolution of irrigated lands
   is limited. The new global historical irrigation data set (HID) provides
   estimates of the temporal development of the area equipped for
   irrigation (AEI) between 1900 and 2005 at 5 arcmin resolution. We
   collected sub-national irrigation statistics from various sources and
   found that the global extent of AEI increased from 63 million ha (Mha)
   in 1900 to 111 Mha in 1950 and 306 Mha in 2005. We developed eight
   gridded versions of time series of AEI by combining sub-national
   irrigation statistics with different data sets on the historical extent
   of cropland and pasture. Different rules were applied to maximize
   consistency of the gridded products to sub-national irrigation
   statistics or to historical cropland and pasture data sets. The HID
   reflects very well the spatial patterns of irrigated land as shown on
   historical maps for the western United States (around year 1900) and on
   a global map (around year 1960). Mean aridity on irrigated land
   increased and mean natural river discharge on irrigated land decreased
   from 1900 to 1950 whereas aridity decreased and river discharge remained
   approximately constant from 1950 to 2005. The data set and its
   documentation are made available in an open-data repository at
   https://mygeohub.org/publications/8 (doi:10.13019/M20599).},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Siebert, S (Corresponding Author), Univ Bonn, Inst Crop Sci \& Resource Conservat, Bonn, Germany.
   Siebert, S., Univ Bonn, Inst Crop Sci \& Resource Conservat, Bonn, Germany.
   Kummu, M.; Porkka, M., Aalto Univ, Water \& Dev Res Grp, Espoo, Finland.
   Doell, P., Univ Frankfurt Main, Inst Phys Geog, Frankfurt, Germany.
   Ramankutty, N., Univ British Columbia, Liu Inst Global Issues, Vancouver, BC V5Z 1M9, Canada.
   Ramankutty, N., Univ British Columbia, Inst Resources Environm \& Sustainabil, Vancouver, BC V5Z 1M9, Canada.
   Scanlon, B. R., Univ Texas Austin, Jackson Sch Geosci, Bureau Econ Geol, Austin, TX 78712 USA.},
DOI = {10.5194/hess-19-1521-2015},
ISSN = {1027-5606},
EISSN = {1607-7938},
Keywords-Plus = {SPATIALLY EXPLICIT; WATER WITHDRAWALS; SURFACE-WATER; MAP; GROUNDWATER;
   RESERVOIRS; CROPLANDS; COVER; AREAS},
Research-Areas = {Geology; Water Resources},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary; Water Resources},
Author-Email = {s.siebert@uni-bonn.de
   matti.kummu@aalto.fi},
Affiliations = {University of Bonn; Aalto University; Goethe University Frankfurt;
   University of British Columbia; University of British Columbia;
   University of Texas System; University of Texas Austin},
ResearcherID-Numbers = {Siebert, Stefan/B-8621-2009
   Kummu, Matti/C-4797-2011
   Ramankutty, Navin/AAM-6074-2020
   Porkka, Miina S/M-6106-2014
   Döll, Petra/A-3784-2009
   Scanlon, Bridget R/A-3105-2009},
ORCID-Numbers = {Siebert, Stefan/0000-0002-9998-0672
   Kummu, Matti/0000-0001-5096-0163
   Ramankutty, Navin/0000-0002-3737-5717
   Porkka, Miina S/0000-0002-8285-6122
   Döll, Petra/0000-0003-2238-4546
   Scanlon, Bridget R/0000-0002-1234-4199},
Funding-Acknowledgement = {Academy of Finland project SCART {[}267463]; Aalto University postdoc
   funds; Maa-ja vesitekniikan tuki ry; Gordon and Betty Moore Foundation
   (through University of Minnesota); GEOSHARE project (USDA)
   {[}59-0210-2-122]},
Funding-Text = {M. Kummu was supported by the Academy of Finland project SCART (grant
   no. 267463) and Aalto University postdoc funds. M. Porkka received
   funding from Maa-ja vesitekniikan tuki ry. A grant to N. Ramankutty from
   the Gordon and Betty Moore Foundation (through a sub-award from the
   University of Minnesota) supported part of this work. S. Siebert and N.
   Ramankutty acknowledge support from the GEOSHARE project (USDA agreement
   no. 59-0210-2-122). We thank Andreas Kunz (Institute of European
   History, University of Mainz) for providing maps and information on the
   administrative set-up in the former German Empire and Lan Zhao (Rosen
   Center for Advanced Computing, Purdue University) for support and
   assistance in the data publishing process. Tim aus der Beek (IWW Water
   Centre, Mulheim, Germany) provided data on the historical extent of
   irrigation in the Aral Sea basin. Kimberly Milligan, Katharina Freydank,
   and Sarah Davidson helped in the collection and digitizing of
   sub-national irrigation statistics.},
Number-of-Cited-References = {72},
Times-Cited = {263},
Usage-Count-Last-180-days = {8},
Usage-Count-Since-2013 = {150},
Journal-ISO = {Hydrol. Earth Syst. Sci.},
Doc-Delivery-Number = {CE9JQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000352160600027},
OA = {gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000794466900001,
Author = {Huang, Xiaojuan and Fu, Yangyang and Wang, Jingjing and Dong, Jie and
   Zheng, Yi and Pan, Baihong and Skakun, Sergii and Yuan, Wenping},
Title = {High-Resolution Mapping of Winter Cereals in Europe by Time Series
   Landsat and Sentinel Images for 2016-2020},
Journal = {REMOTE SENSING},
Year = {2022},
Volume = {14},
Number = {9},
Month = {MAY},
Abstract = {Winter cereals, including wheat, rye, barley, and triticale, are
   important food crops, and it is crucial to identify the distribution of
   winter cereals for monitoring crop growth and predicting yield. The
   production and plating area of winter cereals in Europe both contribute
   12.57\% to the total global cereal production and plating area in 2020.
   However, the distribution maps of winter cereals with high spatial
   resolution are scarce in Europe. Here, we first used synthetic aperture
   radar (SAR) data from Sentinel-1 A/B, in the Interferometric Wide (IW)
   swath mode, to distinguish rapeseed and winter cereals; we then used a
   time-weighted dynamic time warping (TWDTW) method to discriminate winter
   cereals from other crops by comparing the similarity of seasonal changes
   in the Normalized Difference Vegetation Index (NDVI) from Landsat and
   Sentinel-2 images. We generated winter cereal maps for 2016-2020 that
   cover 32 European countries with 30 m spatial resolution. Validation
   using field samples obtained from the Google Earth Engine (GEE) platform
   show that the producer's and user's accuracies are 91\% +/- 7.8\% and
   89\% +/- 10.3\%, respectively, averaged over 32 countries in Europe. The
   winter cereal map agrees well with agricultural census data for planted
   winter cereal areas at municipal and country levels, with the averaged
   coefficient of determination R-2 as 0.77 +/- 0.15 for 2016-2019. In
   addition, our method can identify the distribution of winter cereals two
   months before harvest, with an overall accuracy of 88.4\%, indicating
   that TWDTW is an effective method for timely crop growth monitoring and
   identification at the continent level. The winter cereal maps in Europe
   are available via an open-data repository.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Yuan, WP (Corresponding Author), Sun Yat Sen Univ, Sch Atmospher Sci, Zhuhai 519082, Peoples R China.
   Huang, Xiaojuan; Fu, Yangyang; Zheng, Yi; Pan, Baihong; Yuan, Wenping, Sun Yat Sen Univ, Sch Atmospher Sci, Zhuhai 519082, Peoples R China.
   Wang, Jingjing, Xi An Jiao Tong Univ, Dept Environm Sci \& Engn, State Key Lab Multiphase Flow Power Engn, Xian 710049, Peoples R China.
   Dong, Jie, Zhejiang Univ Water Resources \& Elect Power, Coll Geomat \& Municipal Engn, Hangzhou 310018, Peoples R China.
   Skakun, Sergii, Univ Maryland, Dept Geog Sci, College Pk, MD 20742 USA.},
DOI = {10.3390/rs14092120},
Article-Number = {2120},
EISSN = {2072-4292},
Keywords = {winter cereals; vegetation index; time-weighted dynamic time warping;
   Landsat; Sentinel; Google Earth Engine},
Keywords-Plus = {NATIONAL-SCALE; CROPPING SYSTEMS; RANDOM FOREST; PADDY RICE; NDVI DATA;
   CROPS; WHEAT; AREA; YIELD; ALGORITHM},
Research-Areas = {Environmental Sciences \& Ecology; Geology; Remote Sensing; Imaging
   Science \& Photographic Technology},
Web-of-Science-Categories  = {Environmental Sciences; Geosciences, Multidisciplinary; Remote Sensing;
   Imaging Science \& Photographic Technology},
Author-Email = {huangxj77@mail.sysu.edu.cn
   fuyy23@mail2.sysu.edu.cn
   jjwang@stu.xjtu.edu.cn
   jdongbnu@126.com
   zhengy263@mail2.sysu.edu.cn
   panbh3@mail2.sysu.edu.cn
   skakun@umd.edu
   yuanwp3@mail.sysu.edu.cn},
Affiliations = {Sun Yat Sen University; Xi'an Jiaotong University; Zhejiang University
   of Water Resources and Electric Power; University System of Maryland;
   University of Maryland College Park},
ResearcherID-Numbers = {wang, juan/IUO-6218-2023
   wang, dan/JEF-0836-2023
   WANG, JINGYI/GSJ-1241-2022
   ZHOU, YUE/IZE-6277-2023
   wang, jian/HRB-9588-2023
   wang, jiahui/IXD-1197-2023
   wang, jie/HTQ-4920-2023
   wang, jing/HJA-5384-2022
   Yuan, Wenping/HTM-1454-2023
   wang, xu/IAN-4886-2023
   Wang, Jing/IQW-3496-2023
   wang, jiajun/JRW-6032-2023
   Wang, Jin/GYA-2019-2022
   wang, jing/GRS-7509-2022
   wang, jing/GVT-8700-2022
   },
ORCID-Numbers = {Wang, Jing/0000-0002-8296-2961
   Skakun, Sergii/0000-0002-9039-0174
   Dong, Jie/0000-0002-5742-511X},
Funding-Acknowledgement = {China National Funds for Distinguished Young Scientists {[}41925001];
   National Youth Top-Notch Talent Support Program {[}201548]; Changjiang
   Young Scholars Program of China {[}Q2016161]; Fundamental Research Funds
   for the Central Universities {[}19lgjc02]},
Funding-Text = {This research has been supported by the China National Funds for
   Distinguished Young Scientists (grant no. 41925001), the National Youth
   Top-Notch Talent Support Program (grant no. 201548), the Changjiang
   Young Scholars Program of China (grant no. Q2016161), and the
   Fundamental Research Funds for the Central Universities (grant no.
   19lgjc02).},
Number-of-Cited-References = {55},
Times-Cited = {8},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {62},
Journal-ISO = {Remote Sens.},
Doc-Delivery-Number = {1E4NH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000794466900001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000826076500004,
Author = {Mulligan, Connie J. and Boyer, Doug M. and Turner, Trudy R. and Delson,
   Eric and Leonard, William R.},
Title = {Data sharing in biological anthropology},
Journal = {AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY},
Year = {2022},
Volume = {178},
Number = {74},
Pages = {26-53},
Month = {AUG},
Abstract = {Open data sharing democratizes science by making data more equitably
   available throughout the world. Furthermore, open data sharing improves
   the reproducibility and quality of research and enables new
   collaborations powered by the freely available data. Open data are
   defined as data that can be freely used, reused, and redistributed by
   anyone. For an interdisciplinary field like biological anthropology,
   data sharing is critical since one person cannot easily collect data
   across the domains relevant to our field. The goal of this paper is to
   encourage broader data sharing in our discipline by exploring the state
   of data sharing in the field of biological anthropology. Our paper is
   divided into four parts: the first section describes the benefits,
   challenges, and emerging solutions to open data sharing; the second
   section presents the results of our data archiving and sharing survey
   that was completed by over 700 researchers; the third section presents
   personal experiences of data sharing by the authors; and the fourth
   section discusses the strengths of different types of data repositories
   and provides a list of recommended data repositories.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Mulligan, CJ (Corresponding Author), Univ Florida, Dept Anthropol, Gainesville, FL 32611 USA.
   Mulligan, Connie J., Univ Florida, Dept Anthropol, Gainesville, FL 32611 USA.
   Mulligan, Connie J., Univ Florida, Genet Inst, Gainesville, FL USA.
   Boyer, Doug M., Duke Univ, Dept Evolutionary Anthropol, Durham, NC USA.
   Turner, Trudy R., Univ Wisconsin, Dept Anthropol, Milwaukee, WI 53201 USA.
   Turner, Trudy R., Univ Free State, Dept Genet, Bloemfontein, South Africa.
   Delson, Eric, CUNY, Lehman Coll, Dept Anthropol, Bronx, NY USA.
   Delson, Eric, New York Consortium Evolutionary Primatol, New York, NY USA.
   Leonard, William R., Northwestern Univ, Dept Anthropol, Evanston, IL 60208 USA.},
DOI = {10.1002/ajpa.24499},
ISSN = {2692-7691},
Keywords = {data archiving; data sharing; repositories},
Keywords-Plus = {TSIMANE AMAZONIAN PANEL; EARLY PLEISTOCENE; 1ST RECORD; ACCESS; MIOCENE;
   COLONIZATION; MESOPITHECUS; MORPHOSOURCE; RESEARCHERS; GLASNOST},
Research-Areas = {Anthropology; Evolutionary Biology},
Web-of-Science-Categories  = {Anthropology; Evolutionary Biology},
Author-Email = {cmulligan@ufl.edu},
Affiliations = {State University System of Florida; University of Florida; State
   University System of Florida; University of Florida; Duke University;
   University of Wisconsin System; University of Wisconsin Milwaukee;
   University of the Free State; City University of New York (CUNY) System;
   Lehman College (CUNY); Northwestern University},
ORCID-Numbers = {Mulligan, Connie/0000-0002-4360-2402},
Funding-Acknowledgement = {National Science Foundation {[}BCS 1552848, BCS 1826885, DBI 1661386]},
Funding-Text = {National Science Foundation, Grant/Award Numbers: BCS 1552848, BCS
   1826885, DBI 1661386},
Number-of-Cited-References = {102},
Times-Cited = {7},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Am. J. Biol. Anthropol.},
Doc-Delivery-Number = {2Y7MP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000826076500004},
DA = {2024-01-15},
}

@article{ WOS:000425421500001,
Author = {Sateli, Bahar and Loeffler, Felicitas and Koenig-Ries, Birgitta and
   Witte, Rene},
Title = {ScholarLens: extracting competences from research publications for the
   automatic generation of semantic user profiles},
Journal = {PEERJ COMPUTER SCIENCE},
Year = {2017},
Month = {JUL 3},
Abstract = {Motivation. Scientists increasingly rely on intelligent information
   systems to help them in their daily tasks, in particular for managing
   research objects, like publications or datasets. The relatively young
   research field of Semantic Publishing has been addressing the question
   how scientific applications can be improved through semantically rich
   representations of research objects, in order to facilitate their
   discovery and re-use. To complement the efforts in this area, we propose
   an automatic workflow to construct semantic user profiles of scholars,
   so that scholarly applications, like digital libraries or data
   repositories, can better understand their users' interests, tasks, and
   competences, by incorporating these user profiles in their design. To
   make the user profiles sharable across applications, we propose to build
   them based on standard semantic web technologies, in particular the
   Resource Description Framework (RDF) for representing user profiles and
   Linked Open Data (LOD) sources for representing competence topics. To
   avoid the cold start problem, we suggest to automatically populate these
   profiles by analyzing the publications (co-) authored by users, which we
   hypothesize reflect their research competences.
   Results. We developed a novel approach, ScholarLens, which can
   automatically generate semantic user profiles for authors of scholarly
   literature. For modeling the competences of scholarly users and groups,
   we surveyed a number of existing linked open data vocabularies. In
   accordance with the LOD best practices, we propose an RDF Schema (RDFS)
   based model for competence records that reuses existing vocabularies
   where appropriate. To automate the creation of semantic user profiles,
   we developed a complete, automated workflow that can generate semantic
   user profiles by analyzing full-text research articles through various
   natural language processing (NLP) techniques. In our method, we start by
   processing a set of research articles for a given user. Competences are
   derived by text mining the articles, including syntactic, semantic, and
   LOD entity linking steps. We then populate a knowledge base in RDF
   format with user profiles containing the extracted competences. We
   implemented our approach as an open source library and evaluated our
   system through two user studies, resulting in mean average precision
   (MAP) of up to 95\%. As part of the evaluation, we also analyze the
   impact of semantic zoning of research articles on the accuracy of the
   resulting profiles. Finally, we demonstrate how these semantic user
   profiles can be applied in a number of use cases, including article
   ranking for personalized search and finding scientists competent in a
   topic -e. g., to find reviewers for a paper.},
Publisher = {PEERJ INC},
Address = {341-345 OLD ST, THIRD FLR, LONDON, EC1V 9LL, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Sateli, B (Corresponding Author), Concordia Univ, Semant Software Lab, Dept Comp Sci \& Software Engn, Montreal, PQ, Canada.
   Sateli, Bahar; Witte, Rene, Concordia Univ, Semant Software Lab, Dept Comp Sci \& Software Engn, Montreal, PQ, Canada.
   Loeffler, Felicitas; Koenig-Ries, Birgitta, Friedrich Schiller Univ Jena, Heinz Nixdorf Chair Distributed Informat Syst, Dept Math \& Comp Sci, Jena, Germany.},
DOI = {10.7717/peerj-cs.121},
Article-Number = {e121},
ISSN = {2376-5992},
Keywords = {Natural language processing; Semantic user profile; Semantic publishing;
   Scholarly user modeling; Linked open data},
Keywords-Plus = {REVOLUTION; WEB},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Artificial Intelligence; Computer Science, Information
   Systems; Computer Science, Theory \& Methods},
Author-Email = {sateli@semanticsoftware.info},
Affiliations = {Concordia University - Canada; Friedrich Schiller University of Jena},
ResearcherID-Numbers = {Sateli, Bahar/L-7674-2019
   },
ORCID-Numbers = {Sateli, Bahar/0000-0001-6863-2037
   Loffler, Felicitas/0000-0001-6423-7427},
Funding-Acknowledgement = {NSERC Discovery Grant; DAAD (German Academic Exchange Service) through
   the PPP Canada program; DFG (German Research Foundation) within the
   GFBio project},
Funding-Text = {This work was partially funded by an NSERC Discovery Grant. This work
   was also supported by the DAAD (German Academic Exchange Service)
   through the PPP Canada program and by the DFG (German Research
   Foundation) within the GFBio project. There was no additional external
   funding received for this study. The funders had no role in study
   design, data collection and analysis, decision to publish, or
   preparation of the manuscript.},
Number-of-Cited-References = {55},
Times-Cited = {10},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {17},
Journal-ISO = {PeerJ Comput. Sci.},
Doc-Delivery-Number = {FW6IK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000425421500001},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000945967800006,
Author = {Wu, Mingfang and Richard, Stephen M. and Verhey, Chantelle and Castro,
   Leyla Jael and Cecconi, Baptiste and Juty, Nick},
Title = {An Analysis of Crosswalks from Research Data Schemas to Schema.org},
Journal = {DATA INTELLIGENCE},
Year = {2023},
Volume = {5},
Number = {1},
Pages = {100-121},
Month = {MAR 8},
Abstract = {The increased number of data repositories has greatly increased the
   availability of open data. To enable broad discovery and access to
   research dataset, some data repositories have begun leveraging the web
   architecture by embedding structured metadata markup in dataset web
   landing pages using vocabularies from Schema.org and extensions. This
   paper aims to examine metadata interoperability for supporting global
   data discovery. Specifically, the paper reports a survey on which
   metadata schema has been adopted by participating data repositories, and
   presents an analysis of crosswalks from fourteen research data schemas
   to Schema.org. The analysis indicates most descriptive metadata are
   interoperable among the schemas, the most inconsistent mapping is the
   rights metadata, and a large gap exists in the structural metadata and
   controlled vocabularies to specify various property values. The analysis
   and collated crosswalks can serve as a reference for data repositories
   when they develop crosswalks from their own schemas to Schema.org, and
   provide the research data community a benchmark of structured metadata
   implementation.},
Publisher = {MIT PRESS},
Address = {ONE ROGERS ST, CAMBRIDGE, MA 02142-1209 USA},
Type = {Article},
Language = {English},
Affiliation = {Wu, MF (Corresponding Author), Australian Res Data Commons, Melbourne, Vic 3145, Australia.
   Wu, Mingfang, Australian Res Data Commons, Melbourne, Vic 3145, Australia.
   Richard, Stephen M., US Geosci Informat Network, Neward, DE 19716 USA.
   Verhey, Chantelle, Int Sci Council, World Data Syst, Victoria, BC V8N 1V8, Canada.
   Castro, Leyla Jael, ZB MED Informat Ctr Life Sci, D-50931 Cologne, Germany.
   Cecconi, Baptiste, Observ Paris PSL, Paris Astron Data Ctr, F-75001 Paris, France.
   Juty, Nick, Univ Manchester, Dept Comp Sci, Oxford Rd, Manchester M13 9PL, England.},
DOI = {10.1162/dint\_a\_00186},
EISSN = {2641-435X},
Keywords = {metadata schema; Schema; org; metadata interoperability; FAIR
   (meta)data; metadata schemas crosswalk; research data schemas},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Author-Email = {Mingfang.Wu@ardc.edu.au},
Affiliations = {Universite PSL; Observatoire de Paris; University of Manchester},
ORCID-Numbers = {Wu, Mingfang/0000-0003-1206-3431},
Number-of-Cited-References = {29},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Data Intell.},
Doc-Delivery-Number = {9R9KX},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000945967800006},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000332018400009,
Author = {Torres-Salinas, Daniel and Martin-Martin, Alberto and Fuente-Gutierrez,
   Enrique},
Title = {Analysis of the coverage of the Data Citation Index - Thomson Reuters:
   disciplines, document types and repositories},
Journal = {REVISTA ESPANOLA DE DOCUMENTACION CIENTIFICA},
Year = {2014},
Volume = {37},
Number = {1},
Abstract = {In the past years, the movement of data sharing has been enjoying great
   popularity. Within this context, Thomson Reuters launched at the end of
   2012 a new product inside the Web of Knowledge family: the Data Citation
   Index. The aim of this new database is to enable discovery and access,
   from a single place, to data from a variety of data repositories from
   different subject areas and from around the world. In short note we
   present some results from the analysis of the Data Citation Index.
   Specifically, we address the following issues: discipline coverage, data
   types present in the database and repositories that were included at the
   time of the study.},
Publisher = {CONSEJO SUPERIOR INVESTIGACIONES CIENTIFICAS-CSIC},
Address = {Editorial CSIC, C/VITRUVIO 8, 28006 MADRID, SPAIN},
Type = {Article},
Language = {English},
Affiliation = {Torres-Salinas, D (Corresponding Author), Univ Navarra, Grp Evaluac Ciencia \& Comunicac Cient, Ctr Invest Med Aplicada, E-31080 Pamplona, Spain.
   Torres-Salinas, Daniel, Univ Navarra, Grp Evaluac Ciencia \& Comunicac Cient, Ctr Invest Med Aplicada, E-31080 Pamplona, Spain.
   Martin-Martin, Alberto; Fuente-Gutierrez, Enrique, Univ Granada, Fac Comunicac \& Documentac, Grp Evaluac Ciencia \& Comunicac Cient, E-18071 Granada, Spain.},
DOI = {10.3989/redc.2014.1.1114},
Article-Number = {e036},
ISSN = {0210-0614},
EISSN = {1988-4621},
Keywords = {Data; research data; open access; data sharing; scientific
   communication; databases; citation indexes; Web of Science; Thomson
   Reuters},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {torressalinas@gmail.com
   albertomartin101@gmail.com
   enfun02@gmail.com},
Affiliations = {University of Navarra; University of Granada},
ResearcherID-Numbers = {Torres-Salinas, Daniel/D-5080-2016
   Torres-Salinas, Daniel/A-3968-2010
   Martín-Martín, Alberto/G-3982-2014},
ORCID-Numbers = {Torres-Salinas, Daniel/0000-0002-5648-250X
   Torres-Salinas, Daniel/0000-0001-8790-3314
   Martín-Martín, Alberto/0000-0002-0360-186X},
Number-of-Cited-References = {12},
Times-Cited = {14},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {83},
Journal-ISO = {Rev. Esp. Doc. Cient.},
Doc-Delivery-Number = {AB8CT},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000332018400009},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000595529200003,
Author = {Dong, Jie and Fu, Yangyang and Wang, Jingjing and Tian, Haifeng and Fu,
   Shan and Niu, Zheng and Han, Wei and Zheng, Yi and Huang, Jianxi and
   Yuan, Wenping},
Title = {Early-season mapping of winter wheat in China based on Landsat and
   Sentinel images},
Journal = {EARTH SYSTEM SCIENCE DATA},
Year = {2020},
Volume = {12},
Number = {4},
Pages = {3081-3095},
Month = {NOV 25},
Abstract = {Early-season crop identification is of great importance for monitoring
   crop growth and predicting yield for decision makers and private
   sectors. As one of the largest producers of winter wheat worldwide,
   China outputs more than 18\% of the global production of winter wheat.
   However, there are no distribution maps of winter wheat over a large
   spatial extent with high spatial resolution. In this study, we applied a
   phenology-based approach to distinguish winter wheat from other crops by
   comparing the similarity of the seasonal changes of satellite-based
   vegetation index over all croplands with a standard seasonal change
   derived from known winter wheat fields. Especially, this study examined
   the potential of early-season large-area mapping of winter wheat and
   developed accurate winter wheat maps with 30m spatial resolution for 3
   years (2016-2018) over 11 provinces, which produce more than 98\% of the
   winter wheat in China. A comprehensive assessment based on survey
   samples revealed producer's and user's accuracies higher than 89.30\%
   and 90.59 \%, respectively. The estimated winter wheat area exhibited
   good correlations with the agricultural statistical area data at the
   municipal and county levels. In addition, the earliest identifiable time
   of the geographical location of winter wheat was achieved by the end of
   March, giving a lead time of approximately 3 months before harvest, and
   the optimal identifiable time of winter wheat was at the end of April
   with an overall accuracy of 89.88 \%. These results are expected to aid
   in the timely monitoring of crop growth. The 30m winter wheat maps in
   China are available via an open-data repository (DOI:
   https://doi.org/10.6084/m9.figshare.12003990, Dong et al., 2020a).},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Yuan, WP (Corresponding Author), Sun Yat Sen Univ, Sch Atmospher Sci, Guangzhou 510245, Guangdong, Peoples R China.
   Yuan, WP (Corresponding Author), Southern Marine Sci \& Engn Guangdong Lab, Zhuhai 519000, Guangdong, Peoples R China.
   Dong, Jie, Zhejiang Univ Water Resources \& Elect Power, Coll Geomat \& Municipal Engn, Hangzhou 310018, Zhejiang, Peoples R China.
   Fu, Yangyang; Fu, Shan; Zheng, Yi; Yuan, Wenping, Sun Yat Sen Univ, Sch Atmospher Sci, Guangzhou 510245, Guangdong, Peoples R China.
   Wang, Jingjing, Xi An Jiao Tong Univ, Sch Human Settlements \& Civil Engn, Xian 710049, Shaanxi, Peoples R China.
   Tian, Haifeng, Henan Univ, Coll Environm \& Planning, Kaifeng 475004, Henan, Peoples R China.
   Niu, Zheng, Chinese Acad Sci, Inst Remote Sensing \& Digital Earth, Beijing 100101, Peoples R China.
   Han, Wei, Shandong Gen Stn Agr Technol Extens, Jinan 250013, Shandong, Peoples R China.
   Huang, Jianxi, China Agr Univ, Coll Land Sci \& Technol, Beijing 100083, Peoples R China.
   Yuan, Wenping, Southern Marine Sci \& Engn Guangdong Lab, Zhuhai 519000, Guangdong, Peoples R China.},
DOI = {10.5194/essd-12-3081-2020},
ISSN = {1866-3508},
EISSN = {1866-3516},
Keywords-Plus = {TIME-SERIES; NDVI DATA; CROP; MODIS; YIELD; AREA; CLASSIFICATION; COVER;
   MODEL; PRODUCTIVITY},
Research-Areas = {Geology; Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary; Meteorology \& Atmospheric Sciences},
Author-Email = {yuanwp3@mail.sysu.edu.cn},
Affiliations = {Zhejiang University of Water Resources and Electric Power; Sun Yat Sen
   University; Xi'an Jiaotong University; Henan University; Chinese Academy
   of Sciences; The Institute of Remote Sensing \& Digital Earth, CAS;
   China Agricultural University; Southern Marine Science \& Engineering
   Guangdong Laboratory},
ResearcherID-Numbers = {wang, jing/GRS-7509-2022
   wang, jian/HRB-9588-2023
   wang, dan/JEF-0836-2023
   wang, juan/IUO-6218-2023
   Tian, Haifeng/HLQ-5227-2023
   wang, jie/HTQ-4920-2023
   Huang, Jianxi/AAM-9998-2020
   Wang, Jin/GYA-2019-2022
   wang, jing/HJA-5384-2022
   wang, jing/GVT-8700-2022
   WANG, JINGYI/GSJ-1241-2022
   wang, jiahui/IXD-1197-2023
   Yuan, Wenping/HTM-1454-2023},
ORCID-Numbers = {Tian, Haifeng/0000-0003-4567-2313
   Huang, Jianxi/0000-0003-0341-1983
   },
Funding-Acknowledgement = {China National Funds for Distinguished Young Scientists {[}41925001];
   National Youth Top-Notch Talent Support Program {[}2015-48]; Changjiang
   Young Scholars Program of China {[}Q2016161]; Fundamental Research Funds
   for the Central Universities {[}19lgjc02]},
Funding-Text = {This research has been supported by the China National Funds for
   Distinguished Young Scientists (grant no. 41925001), the National Youth
   Top-Notch Talent Support Program (grant no. 2015-48), the Changjiang
   Young Scholars Program of China (grant no. Q2016161), and the
   Fundamental Research Funds for the Central Universities (grant no.
   19lgjc02).},
Number-of-Cited-References = {62},
Times-Cited = {62},
Usage-Count-Last-180-days = {23},
Usage-Count-Since-2013 = {118},
Journal-ISO = {Earth Syst. Sci. Data},
Doc-Delivery-Number = {PA3HT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000595529200003},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000660250600008,
Author = {Westerveld, Joris J. L. and van den Homberg, Marc J. C. and Nobre,
   Gabriela Guimaraes and van den Berg, Dennis L. J. and Teklesadik, Aklilu
   D. and Stuit, Sjoerd M.},
Title = {Forecasting transitions in the state of food security with machine
   learning using transferable features},
Journal = {SCIENCE OF THE TOTAL ENVIRONMENT},
Year = {2021},
Volume = {786},
Month = {SEP 10},
Abstract = {Food insecurity is a growing concern due to man-made conflicts, climate
   change, and economic downturns. Forecasting the state of food insecurity
   is essential to be able to trigger early actions, for example, by
   humanitarian actors. To measure the actual state of food insecurity,
   expert and consensus-based approaches and surveys are currently used.
   Both require substantial manpower, time, and budget. This paper
   introduces an extreme gradient-boosting machine learning model to
   forecast monthly transitions in the state of food security in Ethiopia,
   at a spatial granularity of livelihood zones, and for lead times of one
   to 12 months, using open-source data. The transition in the state of
   food security, hereafter referred to as predictand, is represented by
   the Integrated Food Security Phase Classification Data. From 19
   categories of datasets, 130 variables were derived and used as
   predictors of the transition in the state of food security. The
   predictors represent changes in climate and land, market, conflict,
   infrastructure, demographics and livelihood zone characteristics. The
   most relevant predictors are found to be food security history and
   surface soil moisture. Overall, the model performs best for forecasting
   Deteriorations and Improvements in the state of food security compared
   to the baselines. The proposed method performs (F1 macro score) at least
   twice as well as the best baseline (a dummy classifier) for a
   Deterioration. The model performs better when forecasting long-term (7
   months; F1 macro average =0.61) compared to short-term (3 months; F1
   macro average = 0.51). Combining machine learning, Integrated Phase
   Classification (IPC) ratings from monitoring systems, and open data can
   add value to existing consensus-based forecasting approaches as this
   combination provides longer lead times and more regular updates. Our
   approach can also be transferred to other countries as most of the data
   on the predictors are openly available from global data repositories.
   (C) 2021 The Author(s). Published by Elsevier B.V.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Westerveld, JJL (Corresponding Author), TNO Def Secur \& Safety, Rijswijk, Netherlands.
   Westerveld, Joris J. L., TNO Def Secur \& Safety, Rijswijk, Netherlands.
   Westerveld, Joris J. L.; Stuit, Sjoerd M., Univ Utrecht, Dept Expt Psychol, Utrecht, Netherlands.
   Westerveld, Joris J. L.; van den Homberg, Marc J. C.; van den Berg, Dennis L. J.; Teklesadik, Aklilu D., 510, Utrecht, Netherlands.
   Teklesadik, Aklilu D., Vrije Univ Brussel, Brussels, Belgium.
   Nobre, Gabriela Guimaraes, Vrije Univ Brussel, Inst Environm Studies IVM, Brussels, Belgium.
   Nobre, Gabriela Guimaraes, World Food Programme, Res Assessment \& Monitoring Div, Rome, Italy.},
DOI = {10.1016/j.scitotenv.2021.147366},
EarlyAccessDate = {MAY 2021},
Article-Number = {147366},
ISSN = {0048-9697},
EISSN = {1879-1026},
Keywords = {Food security; Early warning systems; Open data; Machine learning;
   Extreme gradient boosting; IPC},
Keywords-Plus = {DROUGHT; INSECURITY; AFRICA},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Environmental Sciences},
Author-Email = {Joriswesterveld93@gmail.com},
Affiliations = {Netherlands Organization Applied Science Research; Utrecht University;
   Vrije Universiteit Brussel; Vrije Universiteit Brussel},
ResearcherID-Numbers = {van den Homberg, Marc/AGY-9332-2022},
ORCID-Numbers = {van den Homberg, Marc/0000-0003-1436-254X},
Funding-Acknowledgement = {GFDRR Forecast; Ikea Foundation; Netherlands Red Cross Princess Margriet
   Fund FbF methodologies project},
Funding-Text = {We would like to express our gratitude to Stijn Heemskerk for his
   helpful discussions on the initial model. Marc van den Homberg, Gabriela
   GuimarAes Nobre and Joris Westerveld were partly funded by the GFDRR
   Forecastbased financing for food security project. Marc van den Homberg,
   Aklilu Teklesadik and Joris Westerveld were also partly funded by the
   Ikea Foundation as part of the Innovative Approaches to Response
   Preparedness Program. Marc van den Homberg was also partly funded by the
   Netherlands Red Cross Princess Margriet Fund FbF methodologies project.},
Number-of-Cited-References = {64},
Times-Cited = {21},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {27},
Journal-ISO = {Sci. Total Environ.},
Doc-Delivery-Number = {SQ3IX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000660250600008},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000667684200004,
Author = {Wang, Wei-Chun and Lin, Ting-Yu and Chiu, Sherry Yueh-Hsia and Chen,
   Chiung-Nien and Sarakarn, Pongdech and Ibrahim, Mohd and Chen, Sam
   Li-Sheng and Chen, Hsiu-Hsi and Yeh, Yen-Po},
Title = {Classification of community-acquired outbreaks for the global
   transmission of COVID-19: Machine learning and statistical model
   analysis},
Journal = {JOURNAL OF THE FORMOSAN MEDICAL ASSOCIATION},
Year = {2021},
Volume = {120},
Number = {1},
Pages = {S26-S37},
Month = {JUN},
Abstract = {Background: As Coronavirus disease 2019 (COVID-19) pandemic led to the
   unprecedent largescale repeated surges of epidemics worldwide since the
   end of 2019, data-driven analysis to look into the duration and case
   load of each episode of outbreak worldwide has been motivated.
   Methods: Using open data repository with daily infected, recovered and
   death cases in the period between March 2020 and April 2021, a
   descriptive analysis was performed. The
   susceptible-exposed-infected-recovery model was used to estimate the
   effective productive number (Rt). The duration taken from Rt > 1 to R t
   < 1 and case load were first modelled by using the compound Poisson
   method. Machine learning analysis using the K-means clustering method
   was further adopted to classify patterns of community-acquired outbreaks
   worldwide.
   Results: The global estimated Rt declined after the first surge of
   COVID-19 pandemic but there were still two major surges of epidemics
   occurring in September 2020 and March 2021, respectively, and numerous
   episodes due to various extents of Nonpharmaceutical Interventions
   (NPIs). Unsupervised machine learning identified five patterns as
   ``controlled epidemic{''}, ``mutant propagated epidemic{''},
   ``propagated epidemic{''}, ``persistent epidemic{''} and ``long
   persistent epidemic{''} with the corresponding duration and the
   logarithm of case load from the lowest (18.6 +/- 11.7; 3.4 +/- 1.8)) to
   the highest (258.2 +/- 31.9; 11.9 +/- 2.4). Countries like Taiwan
   outside five clusters were classified as no community-acquired outbreak.
   Conclusion: Data-driven models for the new classification of
   community-acquired outbreaks are useful for global surveillance of
   uninterrupted COVID-19 pandemic and provide a timely decision support
   for the distribution of vaccine and the optimal NPIs from global to
   local community. Copyright (C) 2021, Formosan Medical Association.
   Published by Elsevier Taiwan LLC.},
Publisher = {ELSEVIER TAIWAN},
Address = {RM N-412, 4F, CHIA HSIN BUILDING 11, NO 96, ZHONG SHAN N ROAD SEC 2,
   TAIPEI, 10449, TAIWAN},
Type = {Article},
Language = {English},
Affiliation = {Yeh, YP (Corresponding Author), Changhua Publ Hlth Bur 162,Sec 2,Jhongshan Rd, Changhua 500, Changhua Countr, Taiwan.
   Wang, Wei-Chun; Lin, Ting-Yu; Chen, Hsiu-Hsi; Yeh, Yen-Po, Natl Taiwan Univ, Coll Publ Hlth, Inst Epidemiol \& Prevent Med, Taipei, Taiwan.
   Chiu, Sherry Yueh-Hsia, Chang Gung Univ, Dept Hlth Care Management, Taoyuan, Taiwan.
   Chiu, Sherry Yueh-Hsia, Chang Gung Univ, Hlth Aging Res Ctr, Taoyuan, Taiwan.
   Chen, Chiung-Nien, Natl Taiwan Univ, Ctr Funct Image \& Intervent Therapy, Taipei, Taiwan.
   Chen, Chiung-Nien, Natl Taiwan Univ Hosp, Dept Surg, Taipei, Taiwan.
   Sarakarn, Pongdech, Khon Kaen Univ, Fac Publ Hlth, Epidemiol \& Biostat Dept, Khon Kaen, Thailand.
   Ibrahim, Mohd, Univ Malaysia Sabah, Dept Community \& Family Med, Kota Kinabalu, Sabah, Malaysia.
   Chen, Sam Li-Sheng, Taipei Med Univ, Coll Oral Med, Sch Oral Hyg, Taipei, Taiwan.
   Yeh, Yen-Po, Changhua Publ Hlth Bur, Changhua, Taiwan.},
DOI = {10.1016/j.jfma.2021.05.010},
EarlyAccessDate = {JUN 2021},
ISSN = {0929-6646},
EISSN = {1876-0821},
Keywords = {COVID-19; Machine learning; Cluster analysis; Community-acquired
   outbreak},
Keywords-Plus = {INFLUENZA},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {lgyeh@hotmail.com},
Affiliations = {National Taiwan University; Chang Gung University; Chang Gung
   University; National Taiwan University; National Taiwan University;
   National Taiwan University Hospital; Khon Kaen University; Universiti
   Malaysia Sabah; Taipei Medical University},
ResearcherID-Numbers = {Chen, Sam Li-Sheng/ABE-4605-2020
   },
ORCID-Numbers = {Chen, Sam Li-Sheng/0000-0001-9750-3015
   CHEN, CHIUNG-NIEN/0000-0003-1192-5220
   Yeh, Yen-Po/0000-0002-1091-387X},
Funding-Acknowledgement = {Ministry of Science and Technology, Taiwan {[}MOST 109-2327-B-002-009]},
Funding-Text = {This study was supported by Ministry of Science and Technology, Taiwan
   (MOST 109-2327-B-002-009).},
Number-of-Cited-References = {26},
Times-Cited = {5},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {14},
Journal-ISO = {J. Formos. Med. Assoc.},
Doc-Delivery-Number = {TB1EB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000667684200004},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000832962900020,
Author = {Lanka, Pranav and Yang, Lin and Orive-Miguel, David and Veesa, Joshua
   Deepak and Tagliabue, Susanna and Sudakou, Aleh and Samaei, Saeed and
   Forcione, Mario and Kovacsova, Zuzana and Behera, Anurag and Gladytz,
   Thomas and Grosenick, Dirk and Herve, Lionel and Durduran, Turgut and
   Bejm, Karolina and Morawiec, Magdalena and Kacprzak, Michal and Sawosz,
   Piotr and Gerega, Anna and Liebert, Adam and Belli, Antonio and
   Tachtsidis, Ilias and Lange, Frederic and Bale, Gemma and Baratelli,
   Luca and Gioux, Sylvain and Alexander, Kalyanov and Wolf, Martin and
   Sekar, Sanathana Konugolu Venkata and Zanoletti, Marta and Pirovano,
   Ileana and Lacerenza, Michele and Qiu, Lina and Ferocino, Edoardo and
   Maffeis, Giulia and Amendola, Caterina and Colombo, Lorenzo and
   Frabasile, Lorenzo and Levoni, Pietro and Buttafava, Mauro and Renna,
   Marco and Di Sieno, Laura and Re, Rebecca and Farina, Andrea and
   Spinelli, Lorenzo and Dalla Mora, Alberto and Contini, Davide and
   Taroni, Paola and Tosi, Alberto and Torricelli, Alessandro and Dehghani,
   Hamid and Wabnitz, Heidrun and Pifferi, Antonio},
Title = {Multi-laboratory performance assessment of diffuse optics instruments:
   the BitMap exercise},
Journal = {JOURNAL OF BIOMEDICAL OPTICS},
Year = {2022},
Volume = {27},
Number = {7},
Month = {JUL 1},
Abstract = {Significance: Multi-laboratory initiatives are essential in performance
   assessment and standardization-crucial for bringing biophotonics to
   mature clinical use-to establish protocols and develop reference tissue
   phantoms that all will allow universal instrument comparison.
   Aim: The largest multi-laboratory comparison of performance assessment
   in near-infrared diffuse optics is presented, involving 28 instruments
   and 12 institutions on a total of eight experiments based on three
   consolidated protocols (BIP, MEDPHOT, and NEUROPT) as implemented on
   three kits of tissue phantoms. A total of 20 synthetic indicators were
   extracted from the dataset, some of them defined here anew.
   Approach: The exercise stems from the Innovative Training Network BitMap
   funded by the European Commission and expanded to include other European
   laboratories. A large variety of diffuse optics instruments were
   considered, based on different approaches (time domain/frequency
   domain/continuous wave), at various stages of maturity and designed for
   different applications (e.g., oximetry, spectroscopy, and imaging).
   Results: This study highlights a substantial difference in hardware
   performances (e.g., nine decades in responsivity, four decades in dark
   count rate, and one decade in temporal resolution). Agreement in the
   estimates of homogeneous optical properties was within 12\% of the
   median value for half of the systems, with a temporal stability of <5 \%
   over 1 h, and day-to-day reproducibility of <3 \% . Other tests
   encompassed linearity, crosstalk, uncertainty, and detection of optical
   inhomogeneities.
   Conclusions: This extensive multi-laboratory exercise provides a
   detailed assessment of near-infrared Diffuse optical instruments and can
   be used for reference grading. The dataset-available soon in an open
   data repository-can be evaluated in multiple ways, for instance, to
   compare different analysis tools or study the impact of hardware
   implementations. (C) The Authors. Published by SPIE under a Creative
   Commons Attribution 4.0 International License.},
Publisher = {SPIE-SOC PHOTO-OPTICAL INSTRUMENTATION ENGINEERS},
Address = {1000 20TH ST, PO BOX 10, BELLINGHAM, WA 98225 USA},
Type = {Article},
Language = {English},
Affiliation = {Lanka, P (Corresponding Author), Politecn Milan, Dipartimento Fis, Milan, Italy.
   Wabnitz, H (Corresponding Author), Phys Tech Bundesanstalt PTB, Berlin, Germany.
   Lanka, Pranav; Behera, Anurag; Zanoletti, Marta; Pirovano, Ileana; Lacerenza, Michele; Ferocino, Edoardo; Maffeis, Giulia; Amendola, Caterina; Colombo, Lorenzo; Frabasile, Lorenzo; Levoni, Pietro; Di Sieno, Laura; Re, Rebecca; Dalla Mora, Alberto; Contini, Davide; Taroni, Paola; Torricelli, Alessandro; Pifferi, Antonio, Politecn Milan, Dipartimento Fis, Milan, Italy.
   Yang, Lin; Gladytz, Thomas; Grosenick, Dirk; Wabnitz, Heidrun, Phys Tech Bundesanstalt PTB, Berlin, Germany.
   Orive-Miguel, David; Herve, Lionel, Univ Grenoble Alpes, DTBS, LETI, CEA, Grenoble, France.
   Veesa, Joshua Deepak; Dehghani, Hamid, Univ Birmingham, Sch Comp Sci, Birmingham, W Midlands, England.
   Tagliabue, Susanna; Durduran, Turgut, Inst Photon Sci ICFO, Castelldefels, Spain.
   Sudakou, Aleh; Bejm, Karolina; Morawiec, Magdalena; Kacprzak, Michal; Sawosz, Piotr; Gerega, Anna; Liebert, Adam, Nalecz Inst Biocybernet \& Biomed Engn, Warsaw, Poland.
   Samaei, Saeed; Belli, Antonio, Univ Hosp Birmingham, Natl Inst Hlth Res, Surg Reconstruct \& Microbiol Res Ctr, Birmingham, W Midlands, England.
   Forcione, Mario; Kovacsova, Zuzana; Tachtsidis, Ilias; Lange, Frederic, UCL, Dept Med Phys \& Biomed Engn, London, England.
   Bale, Gemma, Univ Cambridge, Dept Engn, Cambridge, England.
   Bale, Gemma, Univ Cambridge, Dept Phys, Cambridge, England.
   Baratelli, Luca; Gioux, Sylvain, Univ Strasbourg, ICube Lab, Strasbourg, France.
   Alexander, Kalyanov; Wolf, Martin, Univ Hosp Zurich, Dept Neonatol, Biomed Opt Res Lab, Zurich, Switzerland.
   Sekar, Sanathana Konugolu Venkata, Tyndall Natl Inst, IPIC, Cork, Ireland.
   Qiu, Lina, South China Normal Univ, Sch Software, Guangzhou, Peoples R China.
   Buttafava, Mauro; Renna, Marco; Tosi, Alberto, Ist Foton \& Nanotecnol, Milan, Italy.
   Re, Rebecca; Farina, Andrea; Spinelli, Lorenzo, Politecn Milan, Dipartimento Elettron Informaz \& Bioingn, Milan, Italy.},
DOI = {10.1117/1.JBO.27.7.074716},
Article-Number = {074716},
ISSN = {1083-3668},
EISSN = {1560-2281},
Keywords = {diffuse optics; near-infrared spectroscopy; absorption; scattering;
   phantom},
Keywords-Plus = {NEAR-INFRARED SPECTROSCOPY; IN-VIVO; TISSUE; PHANTOM; OXIMETERS; SYSTEM;
   TRIAL},
Research-Areas = {Biochemistry \& Molecular Biology; Optics; Radiology, Nuclear Medicine
   \& Medical Imaging},
Web-of-Science-Categories  = {Biochemical Research Methods; Optics; Radiology, Nuclear Medicine \&
   Medical Imaging},
Author-Email = {sriramapranav.lanka@polimi.it
   heidrun.wabnitz@ptb.de},
Affiliations = {Polytechnic University of Milan; Physikalisch-Technische Bundesanstalt
   (PTB); CEA; Communaute Universite Grenoble Alpes; Universite Grenoble
   Alpes (UGA); University of Birmingham; Barcelona Institute of Science \&
   Technology; Universitat Politecnica de Catalunya; Institut de Ciencies
   Fotoniques (ICFO); Polish Academy of Sciences; Nalecz Institute of
   Biocybernetics \& Biomedical Engineering of the Polish Academy of
   Sciences; University of Birmingham; University of London; University
   College London; University of Cambridge; University of Cambridge;
   Universites de Strasbourg Etablissements Associes; Universite de
   Strasbourg; University of Zurich; University Zurich Hospital; University
   College Cork; South China Normal University; Polytechnic University of
   Milan},
ResearcherID-Numbers = {Gioux, Sylvain/E-8482-2019
   Gerega, Anna/AAR-1496-2021
   Pirovano, Ileana/AEY-7428-2022
   Sekar, Sanathana Konugolu Venkata/P-5123-2017
   Wolf, Max/IRZ-4746-2023
   Belli, Antonio/I-3799-2015
   Veesa, Joshua Deepak/D-6838-2016
   },
ORCID-Numbers = {Gioux, Sylvain/0000-0002-3006-5345
   Gerega, Anna/0000-0002-9809-6041
   Sekar, Sanathana Konugolu Venkata/0000-0003-0912-1282
   Belli, Antonio/0000-0002-3211-9933
   Yang, Lin/0000-0003-3266-6061
   Samaei, Saeed/0000-0001-9399-1840
   lange, Frederic/0000-0001-8561-1879
   Buttafava, Mauro/0000-0002-5446-8026
   Sudakou, Aleh/0000-0003-0508-0495
   Dehghani, Hamid/0000-0003-4117-0412
   Liebert, Adam/0000-0003-1643-7568
   Veesa, Joshua Deepak/0000-0002-0763-7755
   Tachtsidis, Ilias/0000-0002-8125-0313
   Levoni, Pietro/0000-0001-8366-5718},
Funding-Acknowledgement = {European Commission {[}675332]},
Funding-Text = {This work was supported by the European Commission under the ``Brain
   injury and trauma monitoring using advanced photonics{''} (BitMap)
   Horizon 2020 framework program (BitMap, Grant No. 675332)},
Number-of-Cited-References = {68},
Times-Cited = {5},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {J. Biomed. Opt.},
Doc-Delivery-Number = {3I8MG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000832962900020},
OA = {gold, Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001125767900002,
Author = {Li, Kevin and Desai, Riya and Scott, Ryan T. and Steele, Joel Ricky and
   Machado, Meera and Demharter, Samuel and Hoarfrost, Adrienne and Braun,
   Jessica L. and Fajardo, Val A. and Sanders, Lauren M. and Costes,
   Sylvain V.},
Title = {Explainable machine learning identifies multi-omics signatures of muscle
   response to spaceflight in mice},
Journal = {NPJ MICROGRAVITY},
Year = {2023},
Volume = {9},
Number = {1},
Month = {DEC 13},
Abstract = {The adverse effects of microgravity exposure on mammalian physiology
   during spaceflight necessitate a deep understanding of the underlying
   mechanisms to develop effective countermeasures. One such concern is
   muscle atrophy, which is partly attributed to the dysregulation of
   calcium levels due to abnormalities in SERCA pump functioning. To
   identify potential biomarkers for this condition, multi-omics data and
   physiological data available on the NASA Open Science Data Repository
   (osdr.nasa.gov) were used, and machine learning methods were employed.
   Specifically, we used multi-omics (transcriptomic, proteomic, and DNA
   methylation) data and calcium reuptake data collected from C57BL/6 J
   mouse soleus and tibialis anterior tissues during several 30+ day-long
   missions on the international space station. The QLattice symbolic
   regression algorithm was introduced to generate highly explainable
   models that predict either experimental conditions or calcium reuptake
   levels based on multi-omics features. The list of candidate models
   established by QLattice was used to identify key features contributing
   to the predictive capability of these models, with Acyp1 and Rps7
   proteins found to be the most predictive biomarkers related to the
   resilience of the tibialis anterior muscle in space. These findings
   could serve as targets for future interventions aiming to reduce the
   extent of muscle atrophy during space travel.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Sanders, LM; Costes, SV (Corresponding Author), NASA, Ames Res Ctr, Space Biosci Div, Moffett Field, CA 94035 USA.
   Sanders, LM (Corresponding Author), Blue Marble Space, Seattle, WA 98103 USA.
   Li, Kevin; Scott, Ryan T., KBR, Moffett Field, CA USA.
   Li, Kevin, NASA, Space Life Sci Training Program, Moffett Field, CA USA.
   Desai, Riya, Univ Calif Davis, Coll Letters \& Sci, Davis, CA 95616 USA.
   Scott, Ryan T.; Steele, Joel Ricky; Sanders, Lauren M.; Costes, Sylvain V., NASA, Ames Res Ctr, Space Biosci Div, Moffett Field, CA 94035 USA.
   Steele, Joel Ricky, Monash Univ, Monash Biomed Discovery Inst, Monash Prote \& Metabol Platform, Clayton, Vic 3800, Australia.
   Steele, Joel Ricky; Sanders, Lauren M., Blue Marble Space, Seattle, WA 98103 USA.
   Machado, Meera; Demharter, Samuel, Abzu ApS, Copenhagen, Denmark.
   Hoarfrost, Adrienne, Univ Georgia, Dept Marine Sci, Athens, GA 30602 USA.
   Braun, Jessica L.; Fajardo, Val A., Brock Univ, Ctr Bone \& Muscle Hlth, Dept Kinesiol, St Catharines, ON, Canada.},
DOI = {10.1038/s41526-023-00337-5},
Article-Number = {90},
EISSN = {2373-8065},
Keywords-Plus = {ACYLPHOSPHATASE; EXPRESSION; STRESS},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {lauren.m.sanders@nasa.gov
   sylvain.v.costes@nasa.gov},
Affiliations = {National Aeronautics \& Space Administration (NASA); University of
   California System; University of California Davis; National Aeronautics
   \& Space Administration (NASA); NASA Ames Research Center; Monash
   University; University System of Georgia; University of Georgia; Brock
   University},
ORCID-Numbers = {Hoarfrost, Adrienne/0000-0003-1006-9661
   Scott, Ryan/0000-0003-0654-5661},
Funding-Acknowledgement = {NASA High-End Computing (HEC) Program through the NASA Center for
   Climate Simulation (NCCS) at Goddard Space Flight Center; Space Life
   Sciences Training Program - Space Biology Program (Science Mission
   Directorate, Biological and Physical Sciences Division) of the National
   Aeronautics and Space Administration},
Funding-Text = {Resources supporting this work were provided by the NASA High-End
   Computing (HEC) Program through the NASA Center for Climate Simulation
   (NCCS) at Goddard Space Flight Center. We acknowledge support from the
   Space Life Sciences Training Program. The Open Science Data Repository
   is funded by the Space Biology Program (Science Mission Directorate,
   Biological and Physical Sciences Division) of the National Aeronautics
   and Space Administration. Funding for open access charge: NASA.},
Number-of-Cited-References = {38},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {NPJ Microgravity},
Doc-Delivery-Number = {CM8V8},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001125767900002},
OA = {gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000711375900005,
Author = {Askar, Mohsen and Canadas, Raphael Nozal and Svendsen, Kristian},
Title = {An introduction to network analysis for studies of medication use},
Journal = {RESEARCH IN SOCIAL \& ADMINISTRATIVE PHARMACY},
Year = {2021},
Volume = {17},
Number = {12},
Pages = {2054-2061},
Month = {DEC},
Abstract = {Background: Network Analysis (NA) is a method that has been used in
   various disciplines such as Social sciences and Ecology for decades. So
   far, NA has not been used extensively in studies of medication use. Only
   a handful of papers have used NA in Drug Prescription Networks (DPN). We
   provide an introduction to NA terminology alongside a guide to creating
   and extracting results from the medication networks. Objective: To
   introduce the readers to NA as a tool to study medication use by
   demonstrating how to apply different NA measures on 3 generated
   medication networks. Methods: We used the Norwegian Prescription
   Database (NorPD) to create a network that describes the comedication in
   elderly persons in Norway on January 1, 2013. We used the Norwegian
   Electronic Prescription Support System (FEST) to create another network
   of severe drug-drug interactions (DDIs). Lastly, we created a network
   combining the two networks to show the actual use of drugs with severe
   DDIs. We used these networks to elucidate how to apply and interpret
   different network measures in medication networks. Results: Interactive
   network graphs are made available online, Stata and R syntaxes are
   provided. Various useful network measures for medication networks were
   applied such as network topological features, modularity analysis and
   centrality measures. Edge lists data used to generate the networks are
   openly available for readers in an open data repository to explore and
   use. Conclusion: We believe that NA can be a useful tool in medication
   use studies. We have provided information and hopefully inspiration for
   other researchers to use NA in their own projects. While network
   analyses are useful for exploring and discovering structures in
   medication use studies, it also has limitations. It can be challenging
   to interpret and it is not suitable for hypothesis testing.},
Publisher = {ELSEVIER SCIENCE INC},
Address = {STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA},
Type = {Article},
Language = {English},
Affiliation = {Svendsen, K (Corresponding Author), UiT Norges Arktiske Univ, Fac Pharm, Postboks 6050 Langnes, N-9037 Tromso, Norway.
   Askar, Mohsen; Svendsen, Kristian, UiT Arctic Univ Norway, Fac Hlth Sci, Dept Pharm, Tromso, Norway.
   Canadas, Raphael Nozal, UiT Arctic Univ Norway, Fac Sci \& Technol, Dept Informat, Tromso, Norway.},
DOI = {10.1016/j.sapharm.2021.06.021},
EarlyAccessDate = {OCT 2021},
ISSN = {1551-7411},
EISSN = {1934-8150},
Keywords = {Network analysis; Co-medication; Prescriptions; Drug interactions;
   Registries},
Keywords-Plus = {PUBLIC-HEALTH; CENTRALITY; DIFFUSION; TOOL},
Research-Areas = {Public, Environmental \& Occupational Health; Pharmacology \& Pharmacy},
Web-of-Science-Categories  = {Public, Environmental \& Occupational Health; Pharmacology \& Pharmacy},
Author-Email = {kristian.svendsen@uit.no},
Affiliations = {UiT The Arctic University of Tromso; UiT The Arctic University of Tromso},
ORCID-Numbers = {Nozal Canadas, Rafael Adolfo/0000-0001-6492-0218
   Askar, Mohsen/0000-0002-9257-5164
   Svendsen, Kristian/0000-0003-3481-3539},
Number-of-Cited-References = {43},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Res. Soc. Adm. Pharm.},
Doc-Delivery-Number = {WM9CS},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000711375900005},
OA = {Green Published, hybrid, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000366151000007,
Author = {Herrick, Rick and Horton, William and Olsen, Timothy and McKay, Michael
   and Archie, Kevin A. and Marcus, Daniel S.},
Title = {XNAT Central: Open sourcing imaging research data},
Journal = {NEUROIMAGE},
Year = {2016},
Volume = {124},
Number = {B, SI},
Pages = {1093-1096},
Month = {JAN 1},
Abstract = {XNAT Central is a publicly accessible medical imaging data repository
   based on the XNAT open-source imaging informatics platform. It hosts a
   wide variety of research imaging data sets. The primary motivation for
   creating XNAT Central was to provide a central repository to host and
   provide access to a wide variety of neuroimaging data. In this capacity,
   XNAT Central hosts a number of data sets from research labs and
   investigative efforts from around the world, including the OASIS Brains
   imaging studies, the NUSDAST study of schizophrenia, and more. Over
   time, XNAT Central has expanded to include imaging data from many
   different fields of research, including oncology, orthopedics,
   cardiology, and animal studies, but continues to emphasize neuroimaging
   data. Through the use of XNAT's DICOM metadata extraction capabilities,
   XNAT Central provides a searchable repository of imaging data that can
   be referenced by groups, labs, or individuals working in many different
   areas of research. The future development of XNAT Central will be geared
   towards greater ease of use as a reference library of heterogeneous
   neuroimaging data and associated synthetic data. It will also become a
   tool for making data available supporting published research and
   academic articles. (C) 2015 Elsevier Inc. All rights reserved.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Herrick, R (Corresponding Author), Washington Univ, Sch Med, Mallinckrodt Inst Radiol, Neuroinformat Res Grp, Campus Box 8225,4525 Scott Ave, St Louis, MO 63119 USA.
   Herrick, Rick; Horton, William; McKay, Michael; Archie, Kevin A.; Marcus, Daniel S., Washington Univ, Sch Med, Dept Radiol, St Louis, MO 63119 USA.
   Olsen, Timothy, Deck5 Consulting, Normal, IL USA.},
DOI = {10.1016/j.neuroimage.2015.06.076},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords = {XNAT; XNAT Central; Neuroinformatics databases; Open access; Data
   sharing; Open source},
Keywords-Plus = {SOFTWARE},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {rick.herrick@wustl.edu},
Affiliations = {Washington University (WUSTL)},
ResearcherID-Numbers = {McKay, Michael/ABA-9029-2021},
Funding-Acknowledgement = {NIH {[}5 R01 EB009352, U24 RR026057, U54 EB005149, U24 RR025736]},
Funding-Text = {This project was supported by NIH grants 5 R01 EB009352, U24 RR026057,
   U54 EB005149, and U24 RR025736. We wish to thank all contributors to
   XNAT Central, especially the NUSDAST and OASIS projects.},
Number-of-Cited-References = {12},
Times-Cited = {35},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {CY1FB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000366151000007},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000752015800053,
Author = {Bernasconi, Anna and Canakoglu, Arif and Masseroli, Marco and Ceri,
   Stefano},
Title = {META-BASE: A Novel Architecture for Large-Scale Genomic Metadata
   Integration},
Journal = {IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS},
Year = {2022},
Volume = {19},
Number = {1},
Pages = {543-557},
Month = {JAN 1},
Abstract = {The integration of genomic metadata is, at the same time, an important,
   difficult, and well-recognized challenge. It is important because a
   wealth of public data repositories is available to drive biological and
   clinical research; combining information from various heterogeneous and
   widely dispersed sources is paramount to a number of biological
   discoveries. It is difficult because the domain is complex and there is
   no agreement among the various metadata definitions, which refer to
   different vocabularies and ontologies. It is well-recognized in the
   bioinformatics community because, in the common practice, repositories
   are accessed one-by-one, learning their specific metadata definitions as
   result of long and tedious efforts, and such practice is error-prone. In
   this paper, we describe META-BASE, an architecture for integrating
   metadata extracted from a variety of genomic data sources, based upon a
   structured transformation process. We present a variety of innovative
   techniques for data extraction, cleaning, normalization and enrichment.
   We propose a general, open and extensible pipeline that can easily
   incorporate any number of new data sources, and propose the resulting
   repository-already integrating several important sources-which is
   exposed by means of practical user interfaces to respond biological
   researchers' needs.},
Publisher = {IEEE COMPUTER SOC},
Address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA},
Type = {Article},
Language = {English},
Affiliation = {Bernasconi, A (Corresponding Author), Politecn Milan, Dipartimento Elettron Informaz \& Bioingn, Via Ponzio 34-520133, Milan, Italy.
   Bernasconi, Anna; Canakoglu, Arif; Masseroli, Marco; Ceri, Stefano, Politecn Milan, Dipartimento Elettron Informaz \& Bioingn, Via Ponzio 34-520133, Milan, Italy.},
DOI = {10.1109/TCBB.2020.2998954},
ISSN = {1545-5963},
EISSN = {1557-9964},
Keywords = {Data integration; genomic datasets; metadata management; open data;
   bioinformatics},
Keywords-Plus = {DATABASE},
Research-Areas = {Biochemistry \& Molecular Biology; Computer Science; Mathematics},
Web-of-Science-Categories  = {Biochemical Research Methods; Computer Science, Interdisciplinary
   Applications; Mathematics, Interdisciplinary Applications; Statistics \&
   Probability},
Author-Email = {anna.bernasconi@polimi.it
   arif.canakoglu@polimi.it
   marco.masseroli@polimi.it
   stefano.ceri@polimi.it},
Affiliations = {Polytechnic University of Milan},
ResearcherID-Numbers = {bernasconi, anna/AAF-2594-2019
   CANAKOGLU, ARIF/AAE-8340-2019
   },
ORCID-Numbers = {bernasconi, anna/0000-0001-8016-5750
   CANAKOGLU, ARIF/0000-0003-4528-6586
   Ceri, Stefano/0000-0003-0671-2415
   Masseroli, Marco/0000-0003-2574-1174},
Funding-Acknowledgement = {ERC {[}693174 GeCo]},
Funding-Text = {This research was funded by the ERC Advanced Grant 693174 GeCo
   (data-driven Genomic Computing). The authors would like to thank the
   contributions of Alessandro Campi and of the master students Tommaso
   Alfonsi, Andrea Colombo, Federico Gatti, RiccardoMologni, and Jorge
   Ignacio Vera Pena.},
Number-of-Cited-References = {58},
Times-Cited = {14},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {IEEE-ACM Trans. Comput. Biol. Bioinform.},
Doc-Delivery-Number = {YU4LF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000752015800053},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000452704300001,
Author = {Markee, Amanda and Dikow, Torsten},
Title = {Taxonomic revision of the assassin-fly genus <i>Microphontes</i> Londt,
   1994 (Insecta, Diptera, Asilidae)},
Journal = {AFRICAN INVERTEBRATES},
Year = {2018},
Volume = {59},
Number = {2},
Pages = {195-237},
Month = {NOV 30},
Abstract = {The genus Microphontes Londt, 1994 (Diptera: Asilidae: Brachyrhopalinae)
   is revised. Currently, three species are known from Namibia and western
   South Africa, i.e. Microphontes megoura Londt, 1994 from north-western
   South Africa, Microphontes safra Londt, 1994 from Namibia and
   Microphontes whitting-toni Londt, 1994 from western South Africa. Four
   new species, Microphontes ericfisheri sp. n. from the Little Karoo of
   South Africa, Microphontes gaiophanes sp. n. from the Namib desert of
   Namibia and Microphontes jasonlondti sp. n. and Microphontes kryphios
   sp. n. from western South Africa, are described. Distribution,
   occurrence in biodiversity hotspots sensu Conservation International and
   seasonal incidence are discussed. Descriptions/redescriptions,
   photographs and identification keys are provided and made openly
   accessible in data repositories to support future studies of the
   included taxa. An unusual flight pattern of male Microphontes gaiophanes
   sp. n. is discussed. A unique morphological feature on tergite 8 of
   Microphontes females, termed postero-paramedian T8 pores, is described,
   illustrated and discussed.},
Publisher = {COUNCIL NATAL MUSEUM},
Address = {PRIVATE BAG 9070, PIETERMARITZBURG, KWAZULU-NATAL 00000, SOUTH AFRICA},
Type = {Article},
Language = {English},
Affiliation = {Dikow, T (Corresponding Author), Natl Museum Nat Hist, Dept Entomol, Smithsonian Inst, 10 St \& Constitut Ave NW, Washington, DC 20560 USA.
   Markee, Amanda, New Coll Florida, 5800 Bay Shore Rd, Sarasota, FL 34243 USA.
   Dikow, Torsten, Natl Museum Nat Hist, Dept Entomol, Smithsonian Inst, 10 St \& Constitut Ave NW, Washington, DC 20560 USA.},
DOI = {10.3897/AfrInvertebr.59.30684},
ISSN = {1681-5556},
EISSN = {2305-2562},
Keywords = {Assassin fly; robber fly; cybertaxonomy; open-access; male flight
   behaviour; female postero-paramedian T8 pores},
Keywords-Plus = {BIODIVERSITY HOTSPOTS},
Research-Areas = {Entomology; Paleontology; Zoology},
Web-of-Science-Categories  = {Entomology; Paleontology; Zoology},
Author-Email = {DikowT@si.edu},
Affiliations = {State University System of Florida; New College Florida; Smithsonian
   Institution; Smithsonian National Museum of Natural History},
ResearcherID-Numbers = {Dikow, Torsten/H-3103-2019
   },
ORCID-Numbers = {Dikow, Torsten/0000-0003-4816-2909
   Markee, Amanda/0000-0001-7421-6339},
Funding-Acknowledgement = {U.S. National Science Foundation {[}OCE 1560088]; Field Museum of
   Natural History, Chicago, Illinois, under a project entitled,
   ``Exploring enigmatic flies in the Namib desert{''} (2012); NMNH; Global
   Genome Initiative},
Funding-Text = {We would like to thank the museum curators who made specimens available
   through loans. We would also like to graciously acknowledge the U.S.
   National Science Foundation for funding the Research Experience for
   Undergraduates site grant at the NMNH entitled Natural History Research
   Experience (NHRE) (OCE 1560088; PI E. Cottrell, Co-PI E. Hunt). We thank
   Gene Hunt, Virginia Power and Liz Cottrell for their constant support
   during the administration of the NHRE programme. We also acknowledge
   field work support to the junior author through a Field Dreams award
   from the Field Museum of Natural History, Chicago, Illinois, under a
   project entitled, ``Exploring enigmatic flies in the Namib desert{''}
   (2012), the NMNH for a project entitled, ``Novel morphological data to
   decipher the character and life history evolution and diversification of
   Asiloidea and Nemestrinoidea flies{''} (2017), and the Global Genome
   Initiative for a project entitled, ``Asiloid flies in the Nama Karoo and
   comparative phylogenomics{''} (2015). John Hash (NMNH) is thanked for
   taking the photographs of female and male terminalia. Furthermore, we
   thank the Namibian Ministry of Environment and Tourism and CapeNature
   (Western Cape, South Africa) for providing collecting and export permits
   in support of the field work in Namibia and South Africa. We thank
   Rodrigo Vieira and Steve Dennis for their constructive comments during
   peer review and suggestions on biological literature.},
Number-of-Cited-References = {17},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Afr. Invertebr.},
Doc-Delivery-Number = {HD7BG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000452704300001},
OA = {gold, Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000743979700006,
Author = {Li, Chengzan and Zhou, Yuanchun and Zheng, Xiaohuan and Zhang, Zeyu and
   Jiang, Lulu and Li, Zongwen and Wang, Pengyao and Li, Jianhui and Xu,
   Songyuan and Wang, Zhanjie},
Title = {Tracing the footsteps of open research data in China},
Journal = {LEARNED PUBLISHING},
Year = {2022},
Volume = {35},
Number = {1},
Pages = {46-55},
Month = {JAN},
Abstract = {While the scientific research value, economic value and social value of
   research data have become increasingly apparent, the significance of
   open research data has reached a consensus. This article gives an
   introduction to open research data policies and measures in China, and
   reports on the status of constructing necessary infrastructure,
   specifically open data repositories. We compare open data repositories
   in China and Western countries in terms of scale, subject distribution,
   data policies, service and content operations. In addition, this article
   summarizes methods and motivations for data sharing among researchers in
   China. Finally, the paper discusses the characteristics, potential
   problems and challenges of China's open research data practices. We
   conclude with some suggestions for the future development of open
   research data in China from data policy, infrastructure construction,
   compliance with international standards and norms, credibility and
   influence improvement, incentives for data sharing and encouraging data
   sharing research practices.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Li, CZ (Corresponding Author), Chinese Acad Sci, Comp Network Informat Ctr, Beijing 100190, Peoples R China.
   Li, Chengzan; Zhou, Yuanchun; Zhang, Zeyu; Jiang, Lulu; Li, Zongwen; Wang, Pengyao; Li, Jianhui; Xu, Songyuan; Wang, Zhanjie, Chinese Acad Sci, Comp Network Informat Ctr, Beijing 100190, Peoples R China.
   Zheng, Xiaohuan, Chinese Acad Sci, Adm Off, Beijing, Peoples R China.
   Xu, Songyuan; Wang, Zhanjie, Univ Chinese Acad Sci, Beijing, Peoples R China.},
DOI = {10.1002/leap.1439},
ISSN = {0953-1513},
EISSN = {1741-4857},
Keywords = {data sharing; repository; data policies; Science Data Bank},
Keywords-Plus = {POLICIES},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {lichengzan@cnic.cn},
Affiliations = {Chinese Academy of Sciences; Computer Network Information Center, CAS;
   Chinese Academy of Sciences; Chinese Academy of Sciences; University of
   Chinese Academy of Sciences, CAS},
ResearcherID-Numbers = {Zhang, Zeyu/HTO-6741-2023},
Funding-Acknowledgement = {14th Five-year Network Security and Informatization Plan of Chinese
   Academy of Sciences {[}WX145XQ07-03]; Natural Science Foundation of
   China {[}L1924075]; Beijing Nova Program of Science and Technology
   {[}Z191100001119090]},
Funding-Text = {This work was supported by grants from the 14th Five-year Network
   Security and Informatization Plan of Chinese Academy of Sciences (No.
   WX145XQ06), the 14th Five-year Network Security and Informatization Plan
   of Chinese Academy of Sciences (No. WX145XQ07-03), the Natural Science
   Foundation of China (No. 61836013), the Natural Science Foundation of
   China (No. L1924075) and Beijing Nova Program of Science and Technology
   (No. Z191100001119090).},
Number-of-Cited-References = {27},
Times-Cited = {2},
Usage-Count-Last-180-days = {15},
Usage-Count-Since-2013 = {68},
Journal-ISO = {Learn. Publ.},
Doc-Delivery-Number = {YI6TS},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000743979700006},
DA = {2024-01-15},
}

@article{ WOS:000829556200001,
Author = {Bledsoe, Ellen K. and Burant, Joseph B. and Higino, Gracielle T. and
   Roche, Dominique G. and Binning, Sandra A. and Finlay, Kerri and Pither,
   Jason and Pollock, Laura S. and Sunday, Jennifer M. and Srivastava,
   Diane S.},
Title = {Data rescue: saving environmental data from extinction},
Journal = {PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES},
Year = {2022},
Volume = {289},
Number = {1979},
Month = {JUL 27},
Abstract = {Historical and long-term environmental datasets are imperative to
   understanding how natural systems respond to our changing world.
   Although immensely valuable, these data are at risk of being lost unless
   actively curated and archived in data repositories. The practice of data
   rescue, which we define as identifying, preserving, and sharing valuable
   data and associated metadata at risk of loss, is an important means of
   ensuring the long-term viability and accessibility of such datasets.
   Improvements in policies and best practices around data management will
   hopefully limit future need for data rescue; these changes, however, do
   not apply retroactively. While rescuing data is not new, the term lacks
   formal definition, is often conflated with other terms (i.e. data
   reuse), and lacks general recommendations. Here, we outline seven key
   guidelines for effective rescue of historically collected and unmanaged
   datasets. We discuss prioritization of datasets to rescue, forming
   effective data rescue teams, preparing the data and associated metadata,
   and archiving and sharing the rescued materials. In an era of rapid
   environmental change, the best policy solutions will require evidence
   from both contemporary and historical sources. It is, therefore,
   imperative that we identify and preserve valuable, at-risk environmental
   data before they are lost to science.},
Publisher = {ROYAL SOC},
Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bledsoe, EK; Burant, JB; Srivastava, DS (Corresponding Author), Canadian Inst Ecol \& Evolut, Living Data Project, Vancouver, BC, Canada.
   Bledsoe, EK (Corresponding Author), Univ Arizona, Sch Nat Resources \& Environm, Tucson, AZ 85721 USA.
   Bledsoe, EK (Corresponding Author), Univ Regina, Dept Biol, Regina, SK, Canada.
   Burant, JB (Corresponding Author), McGill Univ, Dept Biol, Montreal, PQ, Canada.
   Burant, JB (Corresponding Author), Univ Montreal, Dept Sci Biol, Montreal, PQ, Canada.
   Srivastava, DS (Corresponding Author), Univ British Columbia, Dept Zool, Vancouver, BC, Canada.
   Bledsoe, Ellen K.; Burant, Joseph B.; Higino, Gracielle T.; Roche, Dominique G.; Binning, Sandra A.; Finlay, Kerri; Pither, Jason; Pollock, Laura S.; Sunday, Jennifer M.; Srivastava, Diane S., Canadian Inst Ecol \& Evolut, Living Data Project, Vancouver, BC, Canada.
   Bledsoe, Ellen K., Univ Arizona, Sch Nat Resources \& Environm, Tucson, AZ 85721 USA.
   Bledsoe, Ellen K.; Finlay, Kerri, Univ Regina, Dept Biol, Regina, SK, Canada.
   Burant, Joseph B.; Pollock, Laura S.; Sunday, Jennifer M., McGill Univ, Dept Biol, Montreal, PQ, Canada.
   Burant, Joseph B.; Binning, Sandra A., Univ Montreal, Dept Sci Biol, Montreal, PQ, Canada.
   Higino, Gracielle T.; Srivastava, Diane S., Univ British Columbia, Dept Zool, Vancouver, BC, Canada.
   Higino, Gracielle T.; Srivastava, Diane S., Univ British Columbia, Biodivers Res Ctr, Vancouver, BC, Canada.
   Roche, Dominique G., Carleton Univ, Dept Biol, Ottawa, ON, Canada.
   Roche, Dominique G., Carleton Univ, Inst Environm \& Interdisciplinary Sci, Ottawa, ON, Canada.
   Pither, Jason, Univ British Columbia, Dept Biol, Kelowna, BC, Canada.
   Pither, Jason, Univ British Columbia, Okanagan Inst Biodivers Resilience \& Ecosyst Serv, Kelowna, BC, Canada.},
DOI = {10.1098/rspb.2022.0938},
Article-Number = {20220938},
ISSN = {0962-8452},
EISSN = {1471-2954},
Keywords = {data archiving; historical data; long-term ecological data; open
   science; reproducibility; transparency},
Keywords-Plus = {CONSERVATION; KNOWLEDGE; FUTURE},
Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Environmental Sciences \&
   Ecology; Evolutionary Biology},
Web-of-Science-Categories  = {Biology; Ecology; Evolutionary Biology},
Author-Email = {ebledsoe@arizona.edu
   joseph.burant@mcgill.ca
   srivast@zoology.ubc.ca},
Affiliations = {University of Arizona; University of Regina; McGill University;
   Universite de Montreal; University of British Columbia; University of
   British Columbia; Carleton University; Carleton University; University
   of British Columbia; University of British Columbia},
ResearcherID-Numbers = {Burant, Joey/ABB-2062-2022
   Bledsoe, Ellen K/S-5147-2017
   },
ORCID-Numbers = {Burant, Joey/0000-0002-0713-3100
   Bledsoe, Ellen K/0000-0002-3629-7235
   Srivastava, Diane/0000-0003-4541-5595
   Pither, Jason/0000-0002-7490-6839
   Higino, Gracielle/0000-0003-2791-8383
   Roche, Dominique/0000-0002-3326-864X
   Finlay, Kerri/0000-0001-6835-8832
   Sunday, Jennifer/0000-0001-9372-040X
   Binning, Sandra/0000-0002-2804-9979},
Funding-Acknowledgement = {Collaborative Research and Training Experience (CREATE); Natural
   Sciences and Engineering Research Council of Canada; CREATE grant;
   University of Regina; European Union {[}838237OPTIMISE]},
Funding-Text = {The Living Data Project is funded by a Collaborative Research and
   Training Experience (CREATE) grant to the Canadian Institute of Ecology
   and Evolution from the Natural Sciences and Engineering Research Council
   of Canada. E.K.B., J.B.B. and G.T.H. were supported by the CREATE grant;
   E.K.B. was also supported by the University of Regina. D.G.R. was
   supported by the European Union's Horizon 2020 research and innovation
   programme, under the Marie Sklodowska-Curie grant agreement (no.
   838237OPTIMISE).},
Number-of-Cited-References = {52},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Proc. R. Soc. B-Biol. Sci.},
Doc-Delivery-Number = {3D8OT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000829556200001},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000625207800002,
Author = {Niemitalo, Olli and Koskinen, Eero and Hyvaluoma, Jari and Tahvonen,
   Outi and Lientola, Esa and Lindberg, Henrik and Koskela, Olli and
   Kunttu, Iivari},
Title = {A Year Acquiring and Publishing Drone Aerial Images in Research on
   Agriculture, Forestry, and Private Urban Gardens},
Journal = {TECHNOLOGY INNOVATION MANAGEMENT REVIEW},
Year = {2021},
Volume = {11},
Number = {2},
Pages = {5-16},
Month = {FEB},
Abstract = {Drone imaging has been shown to have increasing value in monitoring and
   analysing different kinds of processes related to agriculture and
   forestry. In long-term monitoring and observation tasks, huge amounts of
   image data are produced and stored. Environmental drone image datasets
   may have value beyond the studies that produced the data. A collection
   of image datasets from multiple data producers can, for example, provide
   more diverse training input for a machine learning model for vegetation
   classification, compared with a single dataset limited in time and
   location. To ensure reproducible research, research data such as image
   datasets should be published in usable and undegraded form, with
   sufficient metadata. Timely storage in a stable research data repository
   is recommended, to avoid loss of data. This work presents research
   datasets of 2020 drone images acquired from agricultural and forestry
   research sites of Hame University of Applied Sciences, and from
   Hameenlinna urban areas. Those images that do not contain personal data
   are made freely available under a Creative Commons Attribution license.
   For images containing personal data, such as images of private homes,
   privacy-preserving forms of data sharingmay be possible in the future.},
Publisher = {CARLETON UNIV GRAPHIC SERVICES},
Address = {DUNTON TOWER RM 2122, 1125 COLONEL BY DR, OTTAWA, ON K1A 5B6, CANADA},
Type = {Article},
Language = {English},
Affiliation = {Niemitalo, O (Corresponding Author), HAMK, Hameenlinna, Finland.
   Niemitalo, Olli; Koskinen, Eero, HAMK, Hameenlinna, Finland.
   Hyvaluoma, Jari; Kunttu, Iivari, Hame Univ Appl Sci, Hameenlinna, Finland.
   Lindberg, Henrik, HAMK, Forest Ecol \& Silviculture, Hameenlinna, Finland.
   Lientola, Esa, HAMK, Forestry, Remote Sensing, Hameenlinna, Finland.
   Koskela, Olli, Hame Univ Appl Sci, Data Sci Team, Hameenlinna, Finland.
   Kunttu, Iivari, Univ Vaasa, Dept Management, Vaasa, Finland.
   Kunttu, Iivari, Nokia Electr Ltd, Espoo, Finland.
   Kunttu, Iivari, TUT, Tampere, Finland.},
DOI = {10.22215/timreview/1418},
ISSN = {1927-0321},
Keywords = {Drone; uav; dataset; open access; agriculture; forestry; gardens;
   multispectral; remote sensing; machine learning},
Research-Areas = {Business \& Economics},
Web-of-Science-Categories  = {Management},
Affiliations = {Hame University of Applied Sciences; Hame University of Applied
   Sciences; Hame University of Applied Sciences; Hame University of
   Applied Sciences; Hame University of Applied Sciences; University of
   Vaasa; Nokia Corporation; Nokia Finland; Tampere University},
ResearcherID-Numbers = {Koskela, Olli/B-5712-2016
   },
ORCID-Numbers = {Koskela, Olli/0000-0002-3424-9969
   Kunttu, Iivari/0000-0002-7460-6422},
Funding-Acknowledgement = {Ministry of Education and Culture (Finland)},
Funding-Text = {This research is part of a Carbon 4.0 research project that has been
   funded by the Ministry of Education and Culture (Finland). The authors
   wish to thank 011i Nevalainen and the anonymous reviewers for their
   feedback, and Roman Tsypin for computation of the image segmentation in
   Figure 7.},
Number-of-Cited-References = {32},
Times-Cited = {3},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Technol. Innov. Manag. Rev.},
Doc-Delivery-Number = {QR4UW},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000625207800002},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000431395900010,
Author = {Bouchard, Kristofer E. and Aimone, James B. and Chun, Miyoung and Dean,
   Thomas and Denker, Michael and Diesmann, Markus and Donofrio, David D.
   and Frank, Loren M. and Kasthuri, Narayanan and Koch, Christof and
   Rubel, Oliver and Simon, Horst D. and Sommer, F. T. and Prabhat},
Title = {International Neuroscience Initiatives through the Lens of
   High-Performance Computing},
Journal = {COMPUTER},
Year = {2018},
Volume = {51},
Number = {4},
Pages = {50-59},
Month = {APR},
Abstract = {Neuroscience initiatives aim to develop new technologies and tools to
   measure and manipulate neuronal circuits. To deal with the massive
   amounts of data generated by these tools, the authors envision the
   co-location of open data repositories in standardized formats together
   with high-performance computing hardware utilizing open source optimized
   analysis codes.},
Publisher = {IEEE COMPUTER SOC},
Address = {10662 LOS VAQUEROS CIRCLE, PO BOX 3014, LOS ALAMITOS, CA 90720-1314 USA},
Type = {Article},
Language = {English},
Affiliation = {Bouchard, KE (Corresponding Author), Lawrence Berkeley Natl Lab, Neural Syst \& Engn Lab, Berkeley, CA 94720 USA.
   Bouchard, KE (Corresponding Author), Univ Calif Berkeley, Helen Wills Neurosci Inst, Berkeley, CA 94720 USA.
   Bouchard, Kristofer E., Lawrence Berkeley Natl Lab, Neural Syst \& Engn Lab, Berkeley, CA 94720 USA.
   Bouchard, Kristofer E.; Sommer, F. T., Univ Calif Berkeley, Helen Wills Neurosci Inst, Berkeley, CA 94720 USA.
   Aimone, James B., Sandia Natl Labs, Ctr Comp Res, Livermore, CA 94550 USA.
   Chun, Miyoung, Kavli Fdn, Sci Programs, Los Angeles, CA USA.
   Dean, Thomas, Google, Mountain View, CA USA.
   Dean, Thomas, Stanford Univ, Computat Neurosci, Stanford, CA 94305 USA.
   Denker, Michael; Diesmann, Markus, Julich Res Ctr, Inst Neurosci \& Med INM 6, Computat \& Syst Neurosci, Julich, Germany.
   Diesmann, Markus, Julich Res Ctr, Inst Adv Simulat IAS 6, Theoret Neurosci, Julich, Germany.
   Donofrio, David D.; Rubel, Oliver; Simon, Horst D.; Prabhat, Lawrence Berkeley Natl Lab, Berkeley, CA USA.
   Frank, Loren M., UC San Francisco, Dept Physiol, San Francisco, CA USA.
   Frank, Loren M., Howard Hughes Med Inst, Chevy Chase, MD USA.
   Kasthuri, Narayanan, Argonne Natl Lab, Argonne, IL 60439 USA.
   Kasthuri, Narayanan, Univ Chicago, Dept Neurobiol, Chicago, IL 60637 USA.
   Koch, Christof, Allen Inst Brain Sci, Washington, DC USA.
   Sommer, F. T., Univ Calif Berkeley, Redwood Ctr Theoret Neurosci, Berkeley, CA USA.},
DOI = {10.1109/MC.2018.2141039},
ISSN = {0018-9162},
EISSN = {1558-0814},
Keywords-Plus = {CODE},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Hardware \& Architecture; Computer Science, Software
   Engineering},
Author-Email = {kebouchard@lbl.gov
   jbaimon@sandia.gov
   chun@kavlifoundation.org
   tld@google.com
   m.denker@fz-juelich.de
   diesmann@fz-juelich.de
   ddonofrio@lbl.gov
   loren@phy.ucsf.edu
   bobbykasthuri@anl.gov
   christofk@alleninstitute.org
   oruebel@lbl.gov
   hdslmon@lbl.gov
   fsommer@berkeley.edu
   prabhat@lbl.gov},
Affiliations = {United States Department of Energy (DOE); Lawrence Berkeley National
   Laboratory; University of California System; University of California
   Berkeley; United States Department of Energy (DOE); Sandia National
   Laboratories; Google Incorporated; Stanford University; Helmholtz
   Association; Research Center Julich; Helmholtz Association; Research
   Center Julich; United States Department of Energy (DOE); Lawrence
   Berkeley National Laboratory; University of California System;
   University of California San Francisco; Howard Hughes Medical Institute;
   United States Department of Energy (DOE); Argonne National Laboratory;
   University of Chicago; Allen Institute for Brain Science; University of
   California System; University of California Berkeley},
ResearcherID-Numbers = {Diesmann, Markus/H-3722-2013
   Denker, Michael/AAV-8066-2021
   Aimone, James/H-4694-2016
   },
ORCID-Numbers = {Diesmann, Markus/0000-0002-2308-5727
   Denker, Michael/0000-0003-1255-7300
   Simon, Horst/0000-0003-0832-3720
   Aimone, James/0000-0002-7361-253X
   Frank, Loren/0000-0002-1752-5677
   Bouchard, Kristofer/0000-0002-1974-4603},
Number-of-Cited-References = {5},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Computer},
Doc-Delivery-Number = {GE7EK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000431395900010},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000800589300043,
Author = {Lee, Jong Eun and Hwang, Minhee and Kim, Yun-Hyeon and Chung, Myung Jin
   and Sim, Byeong Hak and Chae, Kum Ju and Yoo, Jin Young and Jeong, Yeon
   Joo},
Title = {Imaging and Clinical Features of COVID-19 Breakthrough Infections: A
   Multicenter Study},
Journal = {RADIOLOGY},
Year = {2022},
Volume = {303},
Number = {3},
Pages = {682-692},
Month = {JUN},
Abstract = {Background: Since vaccines against COVID-19 became available, rare
   breakthrough infections have been reported despite their high
   efficacies.
   Purpose: To evaluate the clinical and imaging characteristics of
   patients with COVID-19 breakthrough infections and compare them with
   those of unvaccinated patients with COVID-19.
   Materials and Methods: In this retrospective multicenter cohort study,
   the authors analyzed patient (aged >= 18 years) data from three centers
   that were registered in an open data repository for COVID-19 between
   June and August 2021. Hospitalized patients with baseline chest
   radiographs were divided into three groups according to their
   vaccination status. Differences between clinical and imaging features
   were analyzed using the Pearson chi(2) test, Fisher exact test, and
   analysis of variance. Univariable and multivariable logistic regression
   analyses were used to evaluate associations between clinical factors,
   including vaccination status and clinical outcomes.
   Results: Of the 761 hospitalized patients with COVID-19, the mean age
   was 47 years and 385 (51\%) were women; 47 patients (6\%) were fully
   vaccinated (breakthrough infection), 127 (17\%) were partially
   vaccinated, and 587 (77\%) were unvaccinated. Of the 761 patients, 412
   (54\%) underwent chest CT during hospitalization. Among the patients who
   underwent CT, the proportions without pneumonia were 22\% of
   unvaccinated patients (71 of 326), 30\% of partially vaccinated patients
   (19 of 64), and 59\% of fully vaccinated patients (13 of 22) (P < .001).
   Fully vaccinated status was associated with a lower risk of requiring
   supplemental oxygen (odds ratio {[}OR], 0.24 {[}95\% CI: 0.09, 0.64; P
   =.005]) and lower risk of intensive care unit admission (OR, 0.08
   {[}95\% CI: 0.09, 0.78; P =.02]) compared with unvaccinated status.
   Conclusion: Patients with COVID-19 breakthrough infections had a
   significantly higher proportion of CT scans without pneumonia compared
   with unvaccinated patients. Vaccinated patients with breakthrough
   infections had a lower likelihood of requiring supplemental oxygen and
   intensive care unit admission. (C) RSNA, 2022},
Publisher = {RADIOLOGICAL SOC NORTH AMERICA (RSNA)},
Address = {820 JORIE BLVD, SUITE 200, OAK BROOK, ILLINOIS, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Jeong, YJ (Corresponding Author), Pusan Natl Univ Hosp, Dept Radiol, 179 Gudeok Ro, Busan 49241, South Korea.
   Jeong, YJ (Corresponding Author), Pusan Natl Univ Hosp, Biomed Res Inst, 179 Gudeok Ro, Busan 49241, South Korea.
   Lee, Jong Eun; Kim, Yun-Hyeon, Chonnam Natl Univ Hosp, Dept Radiol, Gwangju, South Korea.
   Hwang, Minhee; Jeong, Yeon Joo, Pusan Natl Univ Hosp, Dept Radiol, 179 Gudeok Ro, Busan 49241, South Korea.
   Hwang, Minhee; Jeong, Yeon Joo, Pusan Natl Univ Hosp, Biomed Res Inst, 179 Gudeok Ro, Busan 49241, South Korea.
   Chung, Myung Jin, Sungkyunkwan Univ, Sch Med, Dept Radiol, Samsung Med Ctr, Seoul, South Korea.
   Chung, Myung Jin, Sungkyunkwan Univ, Sch Med, Ctr Imaging Sci, Samsung Med Ctr, Seoul, South Korea.
   Sim, Byeong Hak, Namwon Med Ctr, Dept Radiol, Namwon, South Korea.
   Chae, Kum Ju, Jeonbuk Natl Univ, Res Inst, Jeonbuk Natl Univ Hosp, Dept Radiol,Res Inst Clin Med, Jeonju, South Korea.
   Yoo, Jin Young, Chungbuk Natl Univ Hosp, Dept Radiol, Cheongju, South Korea.},
DOI = {10.1148/radiol.213072},
ISSN = {0033-8419},
Research-Areas = {Radiology, Nuclear Medicine \& Medical Imaging},
Web-of-Science-Categories  = {Radiology, Nuclear Medicine \& Medical Imaging},
Author-Email = {jeongyj0610@gmail.com},
Affiliations = {Chonnam National University; Chonnam National University Hospital; Pusan
   National University; Pusan National University Hospital; Pusan National
   University; Pusan National University Hospital; Sungkyunkwan University
   (SKKU); Samsung Medical Center; Sungkyunkwan University (SKKU); Samsung
   Medical Center; Jeonbuk National University; Jeonbuk National University
   Hospital; Chungbuk National University; Chungbuk National University
   Hospital},
ORCID-Numbers = {Hwang, Minhee/0000-0003-2603-616X
   Chae, Kum Ju/0000-0003-3012-3530
   Sim, Byeong Hak/0000-0003-4779-7355
   Yoo, Jin Young/0000-0003-0007-1960
   Kim, Yun-Hyeon/0000-0002-0047-0729
   Lee, Jong Eun/0000-0002-8754-6801},
Number-of-Cited-References = {32},
Times-Cited = {37},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Radiology},
Doc-Delivery-Number = {1N3WK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000800589300043},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000532403600009,
Author = {Ozturk, Ovunc and Ozacar, Tugba},
Title = {A case study for block-based linked data generation: Recipes as jigsaw
   puzzles},
Journal = {JOURNAL OF INFORMATION SCIENCE},
Year = {2020},
Volume = {46},
Number = {3},
Pages = {419-433},
Month = {JUN},
Abstract = {This article is a proof-of-concept case study to evaluate the
   functionality of a block metaphor-based linked data generator. In this
   work, we chose to produce linked data repository of recipes, which
   provide a medium for people to share their regional and healthy recipes
   with the masses. However, the same approach can also be adapted easily
   to other domains. Therefore, the applicability of our approach extends
   well beyond the food domain that we are considering in this article. As
   a medium for information sharing and understanding between heterogeneous
   systems, ontologies will play an important role in the realisation of
   the Internet of things (IoT) vision. Therefore, an ontology-based recipe
   repository would also be one of the basic blocks of a smart kitchen
   environment. However, building ontologies is a challenging task,
   especially for users who are not conversant in the ontology building
   languages. This article proposes an approach that can be used even by
   non-experts and facilitates the sharing and searching of recipe data. In
   our case, we exploit the features of the block paradigm to publish
   recipes in Linked Data format. In this way, users do not have to know
   the OWL (Web Ontology Language) syntax and the text input is kept
   minimal. As far as we know, this article is the first study that
   produces linked data using Blockly in the literature. We also conducted
   a user-based evaluation of the proposed approach using the System
   Usability Scale (SUS) questionnaire.},
Publisher = {SAGE PUBLICATIONS LTD},
Address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Öztürk, Ö (Corresponding Author), Manisa Celal Bayar Univ, Dept Comp Engn, TR-45140 Manisa, Turkey.
   Ozturk, Ovunc; Ozacar, Tugba, Manisa Celal Bayar Univ, Dept Comp Engn, TR-45140 Manisa, Turkey.},
DOI = {10.1177/0165551519849518},
ISSN = {0165-5515},
EISSN = {1741-6485},
Keywords = {Blockly; cultural heritage; Linked Open Data; ontology; recipe},
Keywords-Plus = {MODEL},
Research-Areas = {Computer Science; Information Science \& Library Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Information Science \& Library
   Science},
Author-Email = {ovunc.ozturk@cbu.edu.tr},
Affiliations = {Celal Bayar University},
ResearcherID-Numbers = {Ozacar, Tugba/C-1349-2012
   Ozturk, Ovunc/H-2154-2011},
ORCID-Numbers = {Ozacar, Tugba/0000-0002-1901-4993
   Ozturk, Ovunc/0000-0001-7127-7902},
Number-of-Cited-References = {38},
Times-Cited = {5},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {16},
Journal-ISO = {J. Inf. Sci.},
Doc-Delivery-Number = {LM7BL},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000532403600009},
DA = {2024-01-15},
}

@article{ WOS:000984611700020,
Author = {Lee, Jong Eun and Hwang, Minhee and Kim, Yun-Hyeon and Chung, Myung Jin
   and Sim, Byeong Hak and Jeong, Won Gi and Jeong, Yeon Joo},
Title = {SARS-CoV-2 Variants Infection in Relationship to Imaging-based Pneumonia
   and Clinical Outcomes},
Journal = {RADIOLOGY},
Year = {2023},
Volume = {306},
Number = {3},
Month = {MAR},
Abstract = {Background: Few reports have evaluated the effect of the SARS-CoV-2
   variant and vaccination on the clinical and imaging features of
   COVID-19.Purpose: To evaluate and compare the effect of vaccination and
   variant prevalence on the clinical and imaging features of infections by
   the SARS-CoV-2.Materials and Methods: Consecutive adults hospitalized
   for confirmed COVID-19 at three centers (two academic medical centers
   and one community hospital) and registered in a nationwide open data
   repository for COVID-19 between August 2021 and March 2022 were
   retrospectively included. All patients had available chest radiographs
   or CT images. Patients were divided into two groups according to
   predominant variant type over the study period. Differences between
   clinical and imaging features were analyzed with use of the Pearson chi
   2 test, Fisher exact test, or the independent t test. Multivariable
   logistic regression analyses were used to evaluate the effect of variant
   predominance and vaccination status on imaging features of pneumonia and
   clinical severity.Results: Of the 2180 patients (mean age, 57 years +/-
   21; 1171 women), 1022 patients (47\%) were treated during the Delta
   variant predominant period and 1158 (53\%) during the Omicron period.
   The Omicron variant prevalence was associated with lower pneumonia
   severity based on CT scores (odds ratio {[}OR], 0.71 {[}95\% CI: 0.51,
   0.99; P = .04]) and lower clinical severity based on intensive care unit
   (ICU) admission or in-hospital death (OR, 0.43 {[}95\% CI: 0.24, 0.77; P
   = .004]) than the Delta variant prevalence. Vaccination was associated
   with the lowest odds of severe pneumonia based on CT scores (OR, 0.05
   {[}95\% CI: 0.03, 0.13; P < .001]) and clinical severity based on ICU
   admission or in-hospital death (OR, 0.15 {[}95\% CI: 0.07, 0.31; P <
   .001]) relative to no vaccination.Conclusion: The SARS-CoV-2 Omicron
   variant prevalence and vaccination were associated with better clinical
   outcomes and lower severe pneumonia risk relative to Delta variant
   prevalence.(c) RSNA, 2022},
Publisher = {RADIOLOGICAL SOC NORTH AMERICA (RSNA)},
Address = {820 JORIE BLVD, SUITE 200, OAK BROOK, ILLINOIS, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Jeong, YJ (Corresponding Author), Pusan Natl Univ, Pusan Natl Univ Yangsan Hosp, Res Inst Convergence Biomed Sci \& Technol, Dept Radiol,Sch Med, 20 Geumo Ro, Yangsan 50612, South Korea.
   Lee, Jong Eun; Kim, Yun-Hyeon, Chonnam Natl Univ Hosp, Dept Radiol, Gwangju, South Korea.
   Hwang, Minhee, Pusan Natl Univ, Pusan Natl Univ Hosp, Dept Radiol, Sch Med, Busan, South Korea.
   Hwang, Minhee, Biomed Res Inst, Busan, South Korea.
   Chung, Myung Jin, Sungkyunkwan Univ, Samsung Med Ctr, Sch Med, Dept Radiol, Seoul, South Korea.
   Chung, Myung Jin, Sungkyunkwan Univ, Ctr Imaging Sci, Samsung Med Ctr, Sch Med, Seoul, South Korea.
   Sim, Byeong Hak, Namwon Med Ctr, Dept Radiol, Namwon, South Korea.
   Jeong, Won Gi, Chonnam Natl Univ, Chonnam Natl Univ Hwasun Hosp, Dept Radiol, Med Sch, Hwasun, South Korea.
   Jeong, Yeon Joo, Pusan Natl Univ, Pusan Natl Univ Yangsan Hosp, Res Inst Convergence Biomed Sci \& Technol, Dept Radiol,Sch Med, 20 Geumo Ro, Yangsan 50612, South Korea.},
DOI = {10.1148/radiol.221795},
Article-Number = {e221795},
ISSN = {0033-8419},
Research-Areas = {Radiology, Nuclear Medicine \& Medical Imaging},
Web-of-Science-Categories  = {Radiology, Nuclear Medicine \& Medical Imaging},
Author-Email = {jeongyj0610@gmail.com},
Affiliations = {Chonnam National University; Chonnam National University Hospital; Pusan
   National University; Pusan National University Hospital; Sungkyunkwan
   University (SKKU); Samsung Medical Center; Sungkyunkwan University
   (SKKU); Samsung Medical Center; Chonnam National University; Chonnam
   National University Hospital; Pusan National University; Pusan National
   University Hospital},
ORCID-Numbers = {Lee, Jong Eun/0000-0002-8754-6801
   Sim, Byeong Hak/0000-0003-4779-7355
   Kim, Yun-Hyeon/0000-0002-0047-0729
   Jeong, Won Gi/0000-0003-2821-2788
   Hwang, Minhee/0000-0003-2603-616X},
Number-of-Cited-References = {22},
Times-Cited = {13},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Radiology},
Doc-Delivery-Number = {F8DZ6},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000984611700020},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000650868600001,
Author = {Orozco-Messana, Javier and Iborra-Lucas, Milagro and Calabuig-Moreno,
   Raimon},
Title = {Neighbourhood Modelling for Urban Sustainability Assessment},
Journal = {SUSTAINABILITY},
Year = {2021},
Volume = {13},
Number = {9},
Month = {MAY},
Abstract = {Climate change is becoming a dominant concern for advanced countries.
   The Paris Agreement sets out a global framework whose implementation
   relates to all human activities and is commonly guided by the United
   Nations Sustainable Development Goals (UN SDGs), which set the scene for
   sustainable development performance configuring all climate action
   related policies. Fast control of CO2 emissions necessarily involves
   cities since they are responsible for 70 percent of greenhouse gas
   emissions. SDG 11 (Sustainable cities and communities) is clearly
   involved in the deployment of SDG 13 (Climate Action). European
   Sustainability policies are financially guided by the European Green
   Deal for a climate neutral urban environment. In turn, a common
   framework for urban policy impact assessment must be based on
   architectural design tools, such as building certification, and common
   data repositories for standard digital building models. Many
   Neighbourhood Sustainability Assessment (NSA) tools have been developed
   but the growing availability of open data repositories for cities,
   together with big-data sources (provided through Internet of Things
   repositories), allow accurate neighbourhood simulations, or in other
   words, digital twins of neighbourhoods. These digital twins are
   excellent tools for policy impact assessment. After a careful analysis
   of current scientific literature, this paper provides a generic approach
   for a simple neighbourhood model developed from building physical
   parameters which meets relevant assessment requirements, while
   simultaneously being updated (and tested) against real open data
   repositories, and how this assessment is related to building
   certification tools. The proposal is validated by real data on energy
   consumption and on its application to the Benicalap neighbourhood in
   Valencia (Spain).},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Orozco-Messana, J (Corresponding Author), Univ Politecn Valencia, Inst Mat Technol ITM, Camino Vera S-N, Valencia 46022, Spain.
   Orozco-Messana, Javier; Calabuig-Moreno, Raimon, Univ Politecn Valencia, Inst Mat Technol ITM, Camino Vera S-N, Valencia 46022, Spain.
   Iborra-Lucas, Milagro, Univ Politecn Valencia, Dept Construcc Arquitecton, Valencia 46022, Spain.},
DOI = {10.3390/su13094654},
Article-Number = {4654},
EISSN = {2071-1050},
Keywords = {neighbourhood sustainability; sustainability assessment; assessment
   tools; building typology},
Keywords-Plus = {LIFE-CYCLE ASSESSMENT; BUILDINGS; LCA},
Research-Areas = {Science \& Technology - Other Topics; Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Green \& Sustainable Science \& Technology; Environmental Sciences;
   Environmental Studies},
Author-Email = {jaormes@cst.upv.es
   miborra1@upvnet.upv.es
   raicamo@arqt.upv.es},
Affiliations = {Universitat Politecnica de Valencia; Universitat Politecnica de Valencia},
ResearcherID-Numbers = {Calabuig Moreno, Raimon/HJY-5812-2023
   Orozco-Messana, Javier/B-3737-2016
   },
ORCID-Numbers = {Orozco-Messana, Javier/0000-0001-8611-8816
   Calabuig-Moreno, Raimon/0000-0003-0810-881X},
Funding-Acknowledgement = {European Commission through the H2020 project ``Green Cities for Climate
   and Water Resilience, Sustainable Economic Growth, Healthy Citizens and
   Environments (GROW GREEN){''} {[}730283]; H2020 Societal Challenges
   Programme {[}730283] Funding Source: H2020 Societal Challenges Programme},
Funding-Text = {This research was co-funded by the European Commission through the H2020
   project ``Green Cities for Climate and Water Resilience, Sustainable
   Economic Growth, Healthy Citizens and Environments (GROW GREEN){''}
   Grant Agreement: 730283.},
Number-of-Cited-References = {23},
Times-Cited = {13},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {38},
Journal-ISO = {Sustainability},
Doc-Delivery-Number = {SC7TO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000650868600001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000426823400003,
Author = {Vazquez, Noe and Vieira, Cristina P. and Amorim, Barbara S. R. and
   Torres, Andre and Lopez-Fernandez, Hugo and Fdez-Riverola, Florentino
   and Sousa, Jose L. R. and Reboiro-Jato, Miguel and Vieira, Jorge},
Title = {Large Scale Analyses and Visualization of Adaptive Amino Acid Changes
   Projects},
Journal = {INTERDISCIPLINARY SCIENCES-COMPUTATIONAL LIFE SCIENCES},
Year = {2018},
Volume = {10},
Number = {1, SI},
Pages = {24-32},
Month = {MAR},
Abstract = {When changes at few amino acid sites are the target of selection,
   adaptive amino acid changes in protein sequences can be identified using
   maximum-likelihood methods based on models of codon substitution (such
   as codeml). Although such methods have been employed numerous times
   using a variety of different organisms, the time needed to collect the
   data and prepare the input files means that tens or hundreds of coding
   regions are usually analyzed. Nevertheless, the recent availability of
   flexible and easy to use computer applications that collect relevant
   data (such as BDBM) and infer positively selected amino acid sites (such
   as ADOPS), means that the entire process is easier and quicker than
   before. However, the lack of a batch option in ADOPS, here reported,
   still precludes the analysis of hundreds or thousands of sequence files.
   Given the interest and possibility of running such large-scale projects,
   we have also developed a database where ADOPS projects can be stored.
   Therefore, this study also presents the B+database, which is both a data
   repository and a convenient interface that looks at the information
   contained in ADOPS projects without the need to download and unzip the
   corresponding ADOPS project file. The ADOPS projects available at B+can
   also be downloaded, unzipped, and opened using the ADOPS graphical
   interface. The availability of such a database ensures results
   repeatability, promotes data reuse with significant savings on the time
   needed for preparing datasets, and effortlessly allows further
   exploration of the data contained in ADOPS projects.},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Vieira, J (Corresponding Author), Univ Porto, Inst Invest Inovacao Saude I3S, Rua Alfredo Allen 208, P-4200135 Porto, Portugal.
   Vieira, J (Corresponding Author), IBMC, Rua Alfredo Allen 208, P-4200135 Porto, Portugal.
   Lopez-Fernandez, Hugo; Fdez-Riverola, Florentino; Reboiro-Jato, Miguel, Univ Vigo, ESEI Escuela Super Ingn Informat, Edificio Politecn,Campus Univ Lagoas S-N, Orense 32004, Spain.
   Vazquez, Noe; Lopez-Fernandez, Hugo; Fdez-Riverola, Florentino; Reboiro-Jato, Miguel, Univ Vigo, CINBIO Ctr Invest Biomed, Campus Univ Lagoas Marcosende, Vigo 36310, Spain.
   Vieira, Cristina P.; Amorim, Barbara S. R.; Torres, Andre; Lopez-Fernandez, Hugo; Sousa, Jose L. R.; Vieira, Jorge, Univ Porto, Inst Invest Inovacao Saude I3S, Rua Alfredo Allen 208, P-4200135 Porto, Portugal.
   Vieira, Cristina P.; Torres, Andre; Lopez-Fernandez, Hugo; Sousa, Jose L. R.; Vieira, Jorge, IBMC, Rua Alfredo Allen 208, P-4200135 Porto, Portugal.
   Amorim, Barbara S. R., INEB, Rua Alfredo Allen 208, P-4200135 Porto, Portugal.},
DOI = {10.1007/s12539-018-0282-7},
ISSN = {1913-2751},
EISSN = {1867-1462},
Keywords = {ADOPS; Positive selection; B plus database; Open data},
Keywords-Plus = {POSITIVELY SELECTED SITES; MAXIMUM-LIKELIHOOD; PHYLOGENETIC ANALYSIS;
   PRUNUS-SPINOSA; EVOLUTION; SELECTION; GENES; VIRUS; HEMAGGLUTININ;
   GLYCOPROTEIN},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {jbvieira@ibmc.up.pt},
Affiliations = {Universidade de Vigo; Universidade de Vigo; CINBIO; Universidade do
   Porto; i3S - Instituto de Investigacao e Inovacao em Saude, Universidade
   do Porto; Universidade do Porto; Universidade do Porto},
ResearcherID-Numbers = {López-Fernández, Hugo/H-7558-2017
   Reboiro-Jato, Miguel/AAB-8453-2022
   Reboiro-Jato, Miguel/G-1102-2011
   Vieira, Jorge/J-7477-2013
   Fdez-Riverola, Florentino/G-1411-2011
   Vieira, Cristina/K-1775-2013
   },
ORCID-Numbers = {López-Fernández, Hugo/0000-0002-6476-7206
   Reboiro-Jato, Miguel/0000-0001-8749-2703
   Reboiro-Jato, Miguel/0000-0001-8749-2703
   Vieira, Jorge/0000-0001-7032-5220
   Fdez-Riverola, Florentino/0000-0002-3943-8013
   Vieira, Cristina/0000-0002-7139-2107
   , IIS Galicia Sur/0000-0003-3812-7413},
Funding-Acknowledgement = {Norte Portugal Regional Operational Programme (NORTE), under the
   PORTUGAL Partnership Agreement, through the European Regional
   Development Fund (FEDER) {[}Norte-01-0145-FEDER-000008]; Spanish
   Ministry of Economy and Competitiveness {[}TIN2013-47153-C3-3-R]; Xunta
   de Galicia},
Funding-Text = {This article is a result of the project Norte-01-0145-FEDER-000008 -
   Porto Neurosciences and Neurologic Disease Research Initiative at I3S,
   supported by Norte Portugal Regional Operational Programme (NORTE 2020),
   under the PORTUGAL 2020 Partnership Agreement, through the European
   Regional Development Fund (FEDER). This work has been also funded by the
   ``Platform of integration of intelligent techniques for analysis of
   biomedical information{''} project (TIN2013-47153-C3-3-R) from Spanish
   Ministry of Economy and Competitiveness. SING group thanks CITI (Centro
   de Investigacion, Transferencia e Innovacion) from University of Vigo
   for hosting its IT infrastructure. H. Lopez-Fernandez is supported by a
   post-doctoral fellowship from Xunta de Galicia.},
Number-of-Cited-References = {29},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Interdiscip. Sci.},
Doc-Delivery-Number = {FY4UY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000426823400003},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000615948300018,
Author = {Luo, Maofang and Xu, Zheping and Hirsch, Tim and Aung, Thant Sin and Xu,
   Wubing and Ji, Liqiang and Qin, Haining and Ma, Keping},
Title = {The use of Global Biodiversity Information Facility (GBIF)-mediated data
   in publications written in Chinese},
Journal = {GLOBAL ECOLOGY AND CONSERVATION},
Year = {2021},
Volume = {25},
Month = {JAN},
Abstract = {With the development of biodiversity informatics, more and more data
   repositories have emerged, providing massive stores of open scientific
   data. The use of open data is increasingly valuable for scientific
   research and related decision making but little is known about which
   topics are addressed, especially in non-English publications. Further,
   how this data should be cited has been called into question. The Global
   Biodiversity Information Facility (GBIF) is the world's largest and most
   widely-used open data access platform on the occurrence of species in
   nature. Here, we analyze the use of GBIF-mediated data in Chinese
   language publications. From 623 publications containing the word
   ``GBIF{''}, we obtained 324 peer-reviewed publications. Among these
   publications, there were 237 journal papers, 17 doctoral theses, 66
   master theses, and 4 conference papers. The publications came from 114
   journals and 49 research institutes and universities. We found that the
   most common topics addressed by these publications were species
   distribution, climate change, biological invasion and medicinal plants.
   For data citation, multiple forms coexist. 295 publications (90\% of
   publications) only cited the name of ``GBIF{''} in the main text,
   without a Digital Object Identifier (DOI). Among the 29 publications
   that cited GBIF in the references, 17 cited the GBIF website, 8
   publications listed the URL of a species page in GBIF, and only 4
   publications cited a DOI, which is what GBIF recommends. Based on a
   discussion on the use of GBIF-mediated data and the resulting data
   citation issues, this study makes three suggestions to improve data
   citation practice, which are applicable to data citation practice in
   other non-English publications. (c) 2020 The Author(s). Published by
   Elsevier B.V. This is an open access article under the CC BY-NC-ND
   license (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Review},
Language = {English},
Affiliation = {Xu, ZP (Corresponding Author), Chinese Acad Sci, Natl Sci Lib, Lab Dynam Semant Publishing Acad Journals \& Knowl, Beijing 100101, Peoples R China.
   Xu, ZP (Corresponding Author), Chinese Acad Sci, Natl Sci Lib, Dept Resource Dev \& Knowledge Org, Beijing 100101, Peoples R China.
   Luo, Maofang; Aung, Thant Sin; Ma, Keping, Chinese Acad Sci, Inst Bot, State Key Lab Vegetat \& Environm Change, Beijing 100093, Peoples R China.
   Xu, Zheping, Chinese Acad Sci, Natl Sci Lib, Lab Dynam Semant Publishing Acad Journals \& Knowl, Beijing 100101, Peoples R China.
   Xu, Zheping, Chinese Acad Sci, Natl Sci Lib, Dept Resource Dev \& Knowledge Org, Beijing 100101, Peoples R China.
   Hirsch, Tim, GBIF Secretariat, Univ Pk 15, DK-2100 Copenhagen O, Denmark.
   Aung, Thant Sin; Ma, Keping, Univ Chinese Acad Sci, Coll Resources \& Environm, Beijing 100049, Peoples R China.
   Xu, Wubing, Aarhus Univ, Ctr Biodivers Dynam Changing World BIOCHANGE, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
   Xu, Wubing, Aarhus Univ, Dept Biol, Sect Ecoinformat \& Biodivers, Ny Munkegade 114, DK-8000 Aarhus C, Denmark.
   Ji, Liqiang, Chinese Acad Sci, Inst Zool, Key Lab Anim Ecol \& Conservat Biol, Beijing 100093, Peoples R China.
   Qin, Haining, Chinese Acad Sci, Inst Bot, State Key Lab Systemat \& Evolut Bot, Beijing 100093, Peoples R China.},
DOI = {10.1016/j.gecco.2020.e01406},
Article-Number = {e01406},
ISSN = {2351-9894},
Keywords = {Biodiversity conservation; Biodiversity informatics; Data citation; FAIR
   data; GBIF},
Research-Areas = {Biodiversity \& Conservation; Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Biodiversity Conservation; Ecology},
Author-Email = {maofang@ibcas.ac.cn
   xuzp@mail.las.ac.cn
   thirsch@gbif.org
   thantsinaung8@ibcas.ac.cn
   wbingxu@gmail.com
   ji@ioz.ac.cn
   hainingqin@ibcas.ac.cn
   kpma@ibcas.ac.cn},
Affiliations = {Chinese Academy of Sciences; Institute of Botany, CAS; Chinese Academy
   of Sciences; National Science Library, CAS; Chinese Academy of Sciences;
   National Science Library, CAS; Chinese Academy of Sciences; University
   of Chinese Academy of Sciences, CAS; Aarhus University; Aarhus
   University; Chinese Academy of Sciences; Chinese Academy of Sciences;
   Institute of Botany, CAS},
ORCID-Numbers = {Xu, Wubing/0000-0002-6566-4452
   Hirsch, Tim/0000-0002-5015-5807
   LUO, Maofang/0000-0003-0929-1273},
Funding-Acknowledgement = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDA19050404]; Talent Introducing Plan in the field of Library and
   Information Science in the Chinese Academy of Sciences},
Funding-Text = {We would like to thank Bureau of International Cooperation, Chinese
   Academy of Sciences and GBIF Secretariat for continuous support of GBIF
   CAS Node since its establishment in 2013. Especially Daniel Noesgaard
   from GBIF Secretariat for his assistance with sorting English language
   publications by Chinese researchers using GBIF-mediated data and Dmitry
   Schigel for comments and suggestions to improve the manuscript. Also,
   thanks to Elizabeth Tokarz from Yale University for her assistance with
   English language and grammatical editing. Thanks to Donald Hobern for
   his helpful comments to improve the manuscript. This study was supported
   by the Strategic Priority Research Program of the Chinese Academy of
   Sciences (Grant No. XDA19050404) and the Talent Introducing Plan in the
   field of Library and Information Science in the Chinese Academy of
   Sciences.},
Number-of-Cited-References = {64},
Times-Cited = {4},
Usage-Count-Last-180-days = {8},
Usage-Count-Since-2013 = {69},
Journal-ISO = {Glob. Ecol. Conserv.},
Doc-Delivery-Number = {QE1EB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000615948300018},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000396150400006,
Author = {Stuermer, Matthias and Abu-Tayeh, Gabriel and Myrach, Thomas},
Title = {Digital sustainability: basic conditions for sustainable digital
   artifacts and their ecosystems},
Journal = {SUSTAINABILITY SCIENCE},
Year = {2017},
Volume = {12},
Number = {2},
Pages = {247-262},
Month = {MAR},
Abstract = {The modern age has heralded a shift from the industrial society, in
   which natural resources are crucial input factors for the economy,
   towards a knowledge society. To date, sustainability literature has
   treated knowledge-and in particular digital artifacts-mainly as a means
   to the end of achieving sustainable development. In this conceptual
   paper, we argue that digital artifacts themselves ought also to be
   considered as resources, which also need to be sustainable. While
   over-consumption is a problem facing natural resources, with sustainable
   digital artifacts, underproduction, and underuse are the biggest
   challenges. In our view, the sustainability of digital artifacts
   improves their potential impact on sustainable development. A
   theoretical foundation for digital artifacts and their ecosystem allows
   us to present the relevant research on digital information, knowledge
   management, digital goods, and innovation literature. Based on these
   insights, we propose ten basic conditions for sustainable digital
   artifacts and their ecosystem to ensure that they provide the greatest
   possible benefit for sustainable development. We then apply those
   characteristics to four exemplary cases: Linux kernel development,
   Bitcoin cryptocurrency, the Wikipedia project, and the Linking Open Drug
   Data repositories. The paper concludes with a research agenda
   identifying topics for sustainability scholars and information systems
   academics, as well as practitioners. A number of suggestions for future
   studies on digital sustainability are also put forward.},
Publisher = {SPRINGER JAPAN KK},
Address = {SHIROYAMA TRUST TOWER 5F, 4-3-1 TORANOMON, MINATO-KU, TOKYO, 105-6005,
   JAPAN},
Type = {Article},
Language = {English},
Affiliation = {Stuermer, M (Corresponding Author), Univ Bern, Bern, Switzerland.
   Stuermer, Matthias; Abu-Tayeh, Gabriel; Myrach, Thomas, Univ Bern, Bern, Switzerland.},
DOI = {10.1007/s11625-016-0412-2},
ISSN = {1862-4065},
EISSN = {1862-4057},
Keywords = {Digital sustainability; Sustainable development; Knowledge commons;
   Linux; Bitcoin; Wikipedia; Linked Open Data},
Keywords-Plus = {OPEN-SOURCE SOFTWARE; PRIVATE-COLLECTIVE INNOVATION; FRAMEWORK;
   ECONOMICS; COPYLEFT; OBJECTS; MODEL; LINUX},
Research-Areas = {Science \& Technology - Other Topics; Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Green \& Sustainable Science \& Technology; Environmental Sciences},
Author-Email = {matthias.stuermer@iwi.unibe.ch},
Affiliations = {University of Bern},
ORCID-Numbers = {Sturmer, Matthias/0000-0001-9038-4041},
Number-of-Cited-References = {90},
Times-Cited = {45},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Sustain. Sci.},
Doc-Delivery-Number = {EN6YX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000396150400006},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000788533800006,
Author = {Chen, Tingting and Chen, Xu and Zhang, Sisi and Zhu, Junwei and Tang,
   Bixia and Wang, Anke and Dong, Lili and Zhang, Zhewen and Yu, Caixia and
   Sun, Yanling and Chi, Lianjiang and Chen, Huanxin and Zhai, Shuang and
   Sun, Yubin and Lan, Li and Zhang, Xin and Xiao, Jingfa and Bao, Yiming
   and Wang, Yanqing and Zhang, Zhang and Zhao, Wenming},
Title = {The Genome Sequence Archive Family: Toward Explosive Data Growth and
   Diverse Data Types},
Journal = {GENOMICS PROTEOMICS \& BIOINFORMATICS},
Year = {2021},
Volume = {19},
Number = {4, SI},
Pages = {578-583},
Month = {AUG},
Abstract = {The Genome Sequence Archive (GSA) is a data repository for archiving raw
   sequence data, which provides data storage and sharing services for
   worldwide scientific communities. Considering explosive data growth with
   diverse data types, here we present the GSA family by expanding into a
   set of resources for raw data archive with different purposes, namely,
   GSA (https://ngdc.cncb.ac.cn/gsa/), GSA for Human (GSA-Human,
   https://ngdc.cncb.ac.cn/gsa-human/), and Open Archive for Miscellaneous
   Data (OMIX, https://ngdc.cncb.ac.cn/omix/). Compared with the 2017
   version, GSA has been significantly updated in data model, online
   functionalities, and web interfaces. GSA-Human, as a new partner of GSA,
   is a data repository specialized in human genetics-related data with
   controlled access and security. OMIX, as a critical complement to the
   two resources mentioned above, is an open archive for miscellaneous
   data. Together, all these resources form a family of resources dedicated
   to archiving explosive data with diverse types, accepting data
   submissions from all over the world, and providing free open access to
   all publicly available data in support of worldwide research activities.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Wang, YQ; Zhang, Z; Zhao, WM (Corresponding Author), China Natl Ctr Bioinformat, Beijing 100101, Peoples R China.
   Wang, YQ; Zhang, Z; Zhao, WM (Corresponding Author), Chinese Acad Sci, Natl Genom Data Ctr, Beijing Inst Genom, Beijing 100101, Peoples R China.
   Wang, YQ; Zhang, Z; Zhao, WM (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Z; Zhao, WM (Corresponding Author), Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Chen, Tingting; Chen, Xu; Zhang, Sisi; Zhu, Junwei; Tang, Bixia; Wang, Anke; Dong, Lili; Zhang, Zhewen; Yu, Caixia; Sun, Yanling; Chi, Lianjiang; Chen, Huanxin; Zhai, Shuang; Sun, Yubin; Lan, Li; Zhang, Xin; Xiao, Jingfa; Bao, Yiming; Wang, Yanqing; Zhang, Zhang; Zhao, Wenming, China Natl Ctr Bioinformat, Beijing 100101, Peoples R China.
   Chen, Tingting; Chen, Xu; Zhang, Sisi; Zhu, Junwei; Tang, Bixia; Wang, Anke; Dong, Lili; Zhang, Zhewen; Yu, Caixia; Sun, Yanling; Chi, Lianjiang; Chen, Huanxin; Zhai, Shuang; Sun, Yubin; Lan, Li; Zhang, Xin; Xiao, Jingfa; Bao, Yiming; Wang, Yanqing; Zhang, Zhang; Zhao, Wenming, Chinese Acad Sci, Natl Genom Data Ctr, Beijing Inst Genom, Beijing 100101, Peoples R China.
   Chen, Tingting; Chen, Xu; Zhang, Sisi; Zhu, Junwei; Tang, Bixia; Wang, Anke; Dong, Lili; Zhang, Zhewen; Yu, Caixia; Sun, Yanling; Chen, Huanxin; Zhai, Shuang; Sun, Yubin; Lan, Li; Zhang, Xin; Xiao, Jingfa; Bao, Yiming; Wang, Yanqing; Zhang, Zhang; Zhao, Wenming, Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Chi, Lianjiang, Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genom \& Precis Med, Beijing 100101, Peoples R China.
   Xiao, Jingfa; Bao, Yiming; Zhang, Zhang; Zhao, Wenming, Univ Chinese Acad Sci, Beijing 100049, Peoples R China.},
DOI = {10.1016/j.gpb.2021.08.001},
ISSN = {1672-0229},
EISSN = {2210-3244},
Keywords = {Genome Sequence Archive; GSA; GSA-Human; OMIX},
Research-Areas = {Genetics \& Heredity},
Web-of-Science-Categories  = {Genetics \& Heredity},
Author-Email = {wangyanqing@big.ac.cn
   zhangzhang@big.ac.cn
   zhaowm@big.ac.cn},
Affiliations = {Chinese Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese
   Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese Academy
   of Sciences; Beijing Institute of Genomics, CAS; Chinese Academy of
   Sciences; University of Chinese Academy of Sciences, CAS},
ResearcherID-Numbers = {zhang, luyu/JJC-4227-2023
   Chen, Huanhuan/HTO-5007-2023
   li, jiaxin/JNT-5073-2023
   chen, huan/GXZ-8858-2022
   lan, lan/JWO-3679-2024
   zhang, zheng/HCH-9684-2022
   cheng, cheng/JBR-8359-2023
   xiao, jing/HRB-7391-2023
   SUN, YANLING/JTT-9082-2023
   zhang, zhang/GQZ-6804-2022
   wang, yanqing/C-5680-2014
   Zhang, Zhang/JAX-2097-2023
   chen, xin/IQW-3432-2023
   },
ORCID-Numbers = {wang, yanqing/0000-0002-3054-3079
   Zhang, Zhang/0000-0001-6603-5060
   Wang, Anke/0000-0002-2565-2334
   sun, yanling/0000-0002-3175-3625
   bixia, tang/0000-0002-9357-4411
   dong, li li/0000-0003-0953-6306
   zhang, si si/0000-0002-3852-4796},
Funding-Acknowledgement = {National Key R\&D Program of China {[}XDB38060100, XDB38030200,
   XDB38050300, XDB38030400, XDA19050302]; Strategic Priority Research
   Program of Chinese Academy of Sciences {[}2017YFC0907502,
   2016YFC0901603, 2017YFC1201202, 2020YFC0847000, 2018YFD1000505]; Chinese
   Academy of Sciences {[}2016YFE0206600, XXH135050-05, XXH-13514-0202];
   Open biodiversity and health big data programme of the internation union
   of biological sciences; National Natural Science Foundation OF China
   {[}153F11KYSB20160008, 32030021];  {[}31871328]},
Funding-Text = {This work was supported by grants from National Key R\&D Program of
   China (Grant No. 2017YFC0907502 to ZZ) ; Strategic Priority Research
   Program of Chinese Academy of Sciences (Grant Nos. XDB38060100 and
   XDB38030200 to YB; XDB38050300 to WZ; XDB38030400 to JX; XDA19050302 to
   ZZ) ; National Key R\&D Program of China (Grant Nos. 2016YFC0901603 to
   WZ; 2017YFC1201202 to YW; 2020YFC0847000 and 2018YFD1000505 to WZ;
   2016YFE0206600 to YB) ; The13th five year informationzation plan of
   chinese academy of sciences (Grant NO. XXH135050-05 to YB) ;Genomics
   Data center construction of chinese academy off sciences (Grant
   NO.xxh-13514-0202 To YB) ;Open biodiversity and health big data
   programme of the internation union of biological sciences to YB; The
   professional association of the alliance of international science
   organizations (Grant No.ANSO-PA-2020-07 TO YB) ;National Natural Science
   Foundation OF China (Grant nos.32030021 and 31871328 to ZZ)
   ;iNTERNATIONAL partnership program of the chinese academy of sciences
   (Grant No.153F11KYSB20160008 to ZZ)},
Number-of-Cited-References = {16},
Times-Cited = {338},
Usage-Count-Last-180-days = {16},
Usage-Count-Since-2013 = {36},
Journal-ISO = {Genom. Proteomics Bioinformatics},
Doc-Delivery-Number = {0V7PV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000788533800006},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000397556400001,
Author = {Brandizi, Marco and Melnichuk, Olga and Bild, Raffael and Kohlmayer,
   Florian and Rodriguez-Castro, Benedicto and Spengler, Helmut and Kuhn,
   Klaus A. and Kuchinke, Wolfgang and Ohmann, Christian and Mustonen, Timo
   and Linden, Mikael and Nyronen, Tommi and Lappalainen, Ilkka and Brazma,
   Alvis and Sarkans, Ugis},
Title = {Orchestrating differential data access for translational research: a
   pilot implementation},
Journal = {BMC MEDICAL INFORMATICS AND DECISION MAKING},
Year = {2017},
Volume = {17},
Month = {MAR 23},
Abstract = {Background: Translational researchers need robust IT solutions to access
   a range of data types, varying from public data sets to pseudonymised
   patient information with restricted access, provided on a case by case
   basis. The reason for this complication is that managing access policies
   to sensitive human data must consider issues of data confidentiality,
   identifiability, extent of consent, and data usage agreements. All these
   ethical, social and legal aspects must be incorporated into a
   differential management of restricted access to sensitive data.
   Methods: In this paper we present a pilot system that uses several
   common open source software components in a novel combination to
   coordinate access to heterogeneous biomedical data repositories
   containing open data ( open access) as well as sensitive data (
   restricted access) in the domain of biobanking and biosample research.
   Our approach is based on a digital identity federation and software to
   manage resource access entitlements.
   Results: Open source software components were assembled and configured
   in such a way that they allow for different ways of restricted access
   according to the protection needs of the data. We have tested the
   resulting pilot infrastructure and assessed its performance, feasibility
   and reproducibility.
   Conclusions: Common open source software components are sufficient to
   allow for the creation of a secure system for differential access to
   sensitive data. The implementation of this system is exemplary for
   researchers facing similar requirements for restricted access data. Here
   we report experience and lessons learnt of our pilot implementation,
   which may be useful for similar use cases. Furthermore, we discuss
   possible extensions for more complex scenarios.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Brandizi, M (Corresponding Author), European Bioinformat Inst EMBL EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Brandizi, Marco; Melnichuk, Olga; Brazma, Alvis; Sarkans, Ugis, European Bioinformat Inst EMBL EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Bild, Raffael; Kohlmayer, Florian; Rodriguez-Castro, Benedicto; Spengler, Helmut; Kuhn, Klaus A., Tech Univ Munich, Univ Med Ctr Rechts Isar, Inst Med Stat \& Epidemiol, Chair Med Informat, Munich, Germany.
   Kuchinke, Wolfgang, Heinrich Heine Univ Dusseldorf, Coordinat Ctr Clin Trials, Dusseldorf, Germany.
   Ohmann, Christian, ECRIN, Dusseldorf, Germany.
   Mustonen, Timo; Linden, Mikael; Nyronen, Tommi; Lappalainen, Ilkka, CSC IT Ctr Sci Ltd, Espoo, Finland.},
DOI = {10.1186/s12911-017-0424-6},
Article-Number = {30},
EISSN = {1472-6947},
Keywords = {Data Access; Translational Research; Clinical Data; Biomedical Data;
   Health Data Protection},
Keywords-Plus = {GENOME-WIDE ASSOCIATION; PHARMACEUTICAL-INDUSTRY; SOMATIC MUTATIONS;
   HEALTH DATA; BIG DATA; PRIVACY; SECURITY; KNOWLEDGE; INFRASTRUCTURE;
   INFORMATION},
Research-Areas = {Medical Informatics},
Web-of-Science-Categories  = {Medical Informatics},
Author-Email = {brandizi@ebi.ac.uk
   ugis@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL); Wellcome Trust Sanger
   Institute; Technical University of Munich; Heinrich Heine University
   Dusseldorf; Finnish IT center for science},
ResearcherID-Numbers = {Ohmann, Christian/AAV-8608-2020
   Brandizi, Marco/X-6605-2019
   Nyrönen, Tommi H./A-3612-2010
   },
ORCID-Numbers = {Brandizi, Marco/0000-0002-5427-2496
   Kohlmayer, Florian/0000-0002-5384-0076
   Brazma, Alvis/0000-0001-5988-7409
   Nyronen, Tommi/0000-0002-5569-5183
   Sarkans, Ugis/0000-0001-9227-8488
   Lappalainen, Ilkka/0000-0001-5762-893X
   Kuchinke, Wolfgang/0000-0002-2809-6900},
Funding-Acknowledgement = {BioMedBridges project (European Commission FP7 Capacities Specific
   Programme) {[}284209]},
Funding-Text = {This work originated from and was funded by the BioMedBridges project
   (European Commission FP7 Capacities Specific Programme, grant agreement
   number 284209).},
Number-of-Cited-References = {101},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {14},
Journal-ISO = {BMC Med. Inform. Decis. Mak.},
Doc-Delivery-Number = {EP7KJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000397556400001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000894722800002,
Author = {Boeschen, Myriam and Le Duc, Diana and Stiller, Mathias and von Laffert,
   Maximilian and Schoeneberg, Torsten and Horn, Susanne},
Title = {Interactive webtool for analyzing drug sensitivity and resistance
   associated with genetic signatures of cancer cell lines},
Journal = {JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY},
Year = {2023},
Volume = {149},
Number = {9},
Pages = {5539-5545},
Month = {AUG},
Abstract = {Purpose A wide therapeutic repertoire has become available to
   oncologists including radio-and chemotherapy, small molecules and
   monoclonal antibodies. However, drug efficacy can be limited by genetic
   heterogeneity. Here, we designed a webtool that facilitates the data
   analysis of the in vitro drug sensitivity data on 265 approved compounds
   from the GDSC database in association with a plethora of genetic changes
   documented for 1001 cell lines in the CCLE data. Methods The webtool
   computes odds ratios of drug resistance for a queried set of genetic
   alterations. It provides results on the efficacy of single compounds or
   groups of compounds assigned to cellular signaling pathways. Webtool
   availability: https://tools.hornlab.org/GDSC/. Results We first
   replicated established associations of genetic driver mutations in BRAF,
   RAS genes and EGFR with drug response. We then tested the ``BRCAness'
   hypothesis and did not find increased sensitivity to the assayed PARP
   inhibitors. Analyzing specific PIK3CA mutations related to cancer and
   mendelian overgrowth, we found support for the described sensitivity of
   H1047 mutants to GSK690693 targeting the AKT pathway. Testing a
   co-mutated gene pair, GATA3 activation abolished PTEN-related
   sensitivity to PI3K/mTOR inhibition. Finally, the pharmacogenomic
   modifier ABCB1 was associated with olaparib resistance. Conclusions This
   tool could identify potential drug candidates in the presence of custom
   sets of genetic changes and moreover, improve the understanding of
   signaling pathways. The underlying computer code can be adapted to
   larger drug response datasets to help structure and accommodate the
   increasingly large biomedical knowledge base.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Boeschen, M; Horn, S (Corresponding Author), Univ Leipzig, Med Fac, Rudolf Schonheimer Inst Biochem, Johannisallee 30, D-04103 Leipzig, Germany.
   Boeschen, M (Corresponding Author), Univ Hosp Leipzig, Inst Pathol, Leipzig, Germany.
   Horn, S (Corresponding Author), Univ Duisburg Essen, Univ Hosp Essen, Dept Dermatol, D-45122 Essen, Germany.
   Horn, S (Corresponding Author), German Canc Consortium DKTK, Partner Site Essen Dusseldorf, D-45122 Essen, Germany.
   Boeschen, Myriam; Schoeneberg, Torsten; Horn, Susanne, Univ Leipzig, Med Fac, Rudolf Schonheimer Inst Biochem, Johannisallee 30, D-04103 Leipzig, Germany.
   Le Duc, Diana, Univ Leipzig, Inst Human Genet, Med Ctr, Leipzig, Germany.
   Boeschen, Myriam; Stiller, Mathias; von Laffert, Maximilian, Univ Hosp Leipzig, Inst Pathol, Leipzig, Germany.
   Horn, Susanne, Univ Duisburg Essen, Univ Hosp Essen, Dept Dermatol, D-45122 Essen, Germany.
   Horn, Susanne, German Canc Consortium DKTK, Partner Site Essen Dusseldorf, D-45122 Essen, Germany.},
DOI = {10.1007/s00432-022-04503-2},
EarlyAccessDate = {DEC 2022},
ISSN = {0171-5216},
EISSN = {1432-1335},
Keywords = {Association test; Candidate compound; Data repository; Discovery
   approach},
Keywords-Plus = {SIGNALING PATHWAY; GENOMICS; DISCOVERY; RESOURCE},
Research-Areas = {Oncology},
Web-of-Science-Categories  = {Oncology},
Author-Email = {Myriam.Boeschen@medizin.uni-leipzig.de
   Susanne.Horn@medizin.uni-leipzig.de},
Affiliations = {Leipzig University; Leipzig University; Leipzig University; University
   of Duisburg Essen; Helmholtz Association; German Cancer Research Center
   (DKFZ)},
ORCID-Numbers = {Boeschen, Myriam/0000-0002-9277-1296},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft (DFG, German Research Foundation) {[}HO
   6389/2-2, KFO 337'-405344257, SFB 1052]; Projekt DEAL},
Funding-Text = {This work was funded by the Deutsche Forschungsgemeinschaft (DFG, German
   Research Foundation) HO 6389/2-2, KFO 337'-405344257 to SH and SFB 1052
   Project B10 to DLD. The funders were not involved in study design, data
   collection and analysis, decision to publish, or preparation of the
   manuscript. Open Access funding enabled and organized by Projekt DEAL.},
Number-of-Cited-References = {22},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Cancer Res. Clin. Oncol.},
Doc-Delivery-Number = {U4PM3},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000894722800002},
OA = {Green Submitted, Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000458307000001,
Author = {Dedeurwaerdere, Tom and Melindi-Ghidi, Paolo and Sas, Willem},
Title = {Networked innovation and coalition formation: the effect of group-based
   social preferences},
Journal = {ECONOMICS OF INNOVATION AND NEW TECHNOLOGY},
Year = {2018},
Volume = {27},
Number = {7},
Pages = {577-593},
Abstract = {In this paper, we study the production and dissemination of public
   knowledge goods, such as technological knowledge, generated by a network
   of voluntarily cooperating innovators. We develop a private-collective
   model of public knowledge production in networked innovation systems,
   where group-based social preferences have an impact on the coalition
   formation of developers. Our model builds on the large empirical
   literature on voluntary production of pooled public knowledge goods,
   including source code in communities of software developers or data
   provided to open access data repositories. Our analysis shows under
   which conditions social preferences, such as `group belonging' or `peer
   approval', influence the stable coalition size, as such rationalising
   several stylized facts emerging from large-scale surveys of open-source
   software developers, previously unaccounted for. Furthermore,
   heterogeneity of social preferences is added to the model to study the
   formation of stable but mixed coalitions.},
Publisher = {ROUTLEDGE JOURNALS, TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Melindi-Ghidi, P (Corresponding Author), Univ Strasbourg, BETA, Strasbourg, France.
   Dedeurwaerdere, Tom, Catholic Univ Louvain, Louvain La Neuve, Belgium.
   Dedeurwaerdere, Tom, FNRS, Brussels, Belgium.
   Melindi-Ghidi, Paolo, Univ Strasbourg, BETA, Strasbourg, France.
   Melindi-Ghidi, Paolo, Univ Paris Nanterre, EconomiX, Nanterre, France.
   Sas, Willem, Univ Stirling, Econ Div, Stirling, Scotland.
   Sas, Willem, Katholieke Univ Leuven, Dept Econ, Leuven, Belgium.
   Melindi-Ghidi, Paolo, Univ Aix \& Marseille, Greqam, Marseille, France.},
DOI = {10.1080/10438599.2017.1378163},
ISSN = {1043-8599},
EISSN = {1476-8364},
Keywords = {Coalition formation; networked innovation; open-source software (OSS);
   public knowledge goods; private-collective model; social preferences},
Keywords-Plus = {OPEN-SOURCE SOFTWARE; INTERNATIONAL ENVIRONMENTAL AGREEMENTS;
   PRIVATE-COLLECTIVE INNOVATION; PUBLIC-GOODS; INTERORGANIZATIONAL
   COLLABORATION; KNOWLEDGE; PROVISION; COOPERATION; UNCERTAINTY; MODEL},
Research-Areas = {Business \& Economics},
Web-of-Science-Categories  = {Economics},
Author-Email = {melindighidi@unistra.fr},
Affiliations = {Universite Catholique Louvain; Fonds de la Recherche Scientifique -
   FNRS; Universites de Strasbourg Etablissements Associes; Universite de
   Strasbourg; University of Stirling; KU Leuven; Aix-Marseille Universite},
ResearcherID-Numbers = {Sas, Willem/JFA-6990-2023
   },
ORCID-Numbers = {melindi-ghidi, paolo/0000-0002-0708-9621},
Funding-Acknowledgement = {European Commission {[}28758, 282625, 284]; National Science Foundation;
   A{*}MIDEX project by the Investissements d'Avenir{''}French Government
   program {[}ANR-11-IDEX-0001-02]; FamPol project by the Investissements
   d'Avenir{''}French Government program {[}ANR-14-FRAL-0007]; `Steunpunt
   Beleidsrelevant Onderzoek Fiscaliteit en Begroting' - Flemish
   government; Agence Nationale de la Recherche (ANR) {[}ANR-14-FRAL-0007]
   Funding Source: Agence Nationale de la Recherche (ANR)},
Funding-Text = {We gratefully acknowledge co-funding from the European Commission, under
   the contract of three PF7-projects, including MICRO B3 (grant agreement
   28758), BIOMOT (grant agreement 282625), GENCOMMONS (ERC grant agreement
   284) and co-funding from the National Science Foundation (MIS Global
   Science Commons). Melindi-Ghidi gratefully acknowledges the support of
   the A{*}MIDEX project (n. ANR-11-IDEX-0001-02) and the FamPol project
   (n. ANR-14-FRAL-0007), both funded by the Investissements
   d'Avenir{''}French Government program, managed by the French National
   Research Agency (ANR). Sas thankfully recognises the financial support
   of the `Steunpunt Beleidsrelevant Onderzoek Fiscaliteit en Begroting',
   funded by the Flemish government.},
Number-of-Cited-References = {62},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Econ. Innov. New Technol.},
Doc-Delivery-Number = {HK9JJ},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000458307000001},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000416984300012,
Author = {Rabinowitz, Jonathan and Schooler, Nina R. and Anderson, Ariana and
   Ayearst, Lindsay and Daniel, David and Davidson, Michael and Khan,
   Anzalee and Kinon, Bruce and Menard, Francois and Opler, Lewis and
   Opler, Mark and Severe, Joanne B. and Williamson, David and Yavorsky,
   Christian and Zhao, Jun and ISCTM ALGORITHMS FLAGS},
Title = {Consistency checks to improve measurement with the Positive and Negative
   Syndrome Scale (PANSS)},
Journal = {SCHIZOPHRENIA RESEARCH},
Year = {2017},
Volume = {190},
Pages = {74-76},
Month = {DEC},
Abstract = {International Society for CNS Clinical Trials and Methodology convened
   an expert working-group that assembled consistency/inconsistency flags
   for the Positive and Negative Syndrome Scale (PANSS). Twenty-four flags
   were identified and divided based on extent to which they represent
   error (Possibly, Probably, Very probably or definitely). The flags were
   applied to assessments derived from the NEWMEDS data repository and the
   CATIE clinical trial data. Almost 40\% of ratings had at least one
   inconsistency flag raised and 10\% had two. Application of flags to
   clinical rating can improve reliability and validity of trials. (C) 2017
   The Authors. Published by Elsevier B.V. This is an open access article
   under the CC BY-NC-ND license
   (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
Publisher = {ELSEVIER SCIENCE BV},
Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Rabinowitz, J (Corresponding Author), Bar Ilan Univ, Ramat Gan, Israel.
   Rabinowitz, Jonathan, Bar Ilan Univ, Ramat Gan, Israel.
   Schooler, Nina R., Suny Downstate Med Ctr, Brooklyn, NY 11203 USA.
   Anderson, Ariana, Univ Calif Los Angeles, Dept Psychiat \& Biobehav Sci, 760 Westwood Plaza,Ste 28-224, Los Angeles, CA 90095 USA.
   Ayearst, Lindsay, Multihlth Syst Inc, Res \& Dev, Clin Educ Publ Safety Div, 3770 Victoria Pk Ave, Toronto, ON M2H 3M6, Canada.
   Daniel, David, Bracket Global LLC, POB 7137, Mclean, VA 22106 USA.
   Davidson, Michael, Tel Aviv Univ, Tel Aviv, Israel.
   Khan, Anzalee, Nathan S Kline Inst Psychiat Res, 140 Old Orangeburg Rd, Orangeburg, NY 10962 USA.
   Kinon, Bruce, Lundbeck LLC, 6 Pkwy North,Suite 400, Deerfield, IL 60015 USA.
   Menard, Francois, Grp Hosp Cochin, Pavillon TARNIER,27 Rue Faubourg St Jacques, Paris, France.
   Opler, Lewis, Long Isl Univ, 1 Univ Plaza, Brooklyn, NY 11201 USA.
   Opler, Mark, ProPhase LLC, 3 Pk Ave, New York, NY 10016 USA.
   Opler, Mark, NYU Sch Med, Dept Psychiat, 1 Pk Ave, New York, NY 10016 USA.
   Severe, Joanne B., 11629 Danville Dr, Rockville, MD 20852 USA.
   Williamson, David, Janssen Sci Affairs LLC, 1125 Trenton Harbourton Rd, Titusville, NJ 08560 USA.
   Yavorsky, Christian, Cronos CCS, 201 South Main St, Lambertville, NJ 08530 USA.
   Zhao, Jun, Abbvie Pharma, R436,Bldg AP9A-2,1 North Waukegan Rd, N Chicago, IL 60064 USA.},
DOI = {10.1016/j.schres.2017.03.017},
ISSN = {0920-9964},
EISSN = {1573-2509},
Keywords-Plus = {SCHIZOPHRENIA},
Research-Areas = {Psychiatry},
Web-of-Science-Categories  = {Psychiatry},
Author-Email = {Jonathan.Rabinowitz@biu.ac.il},
Affiliations = {Bar Ilan University; State University of New York (SUNY) System; State
   University of New York (SUNY) Downstate Medical Center; University of
   California System; University of California Los Angeles; Tel Aviv
   University; Nathan Kline Institute for Psychiatric Research; Lundbeck
   Corporation; Assistance Publique Hopitaux Paris (APHP); Universite Paris
   Cite; Hopital Universitaire Cochin - APHP; Long Island
   University-Brooklyn Campus; New York University; Johnson \& Johnson;
   Janssen Pharmaceuticals},
ResearcherID-Numbers = {Rabinowitz, Jonathan/AAG-3708-2021
   Opler, Mark/U-7075-2019
   Rabinowitz, Jonathan/K-8480-2015
   Ayearst, Lindsay E./AAO-5518-2021
   Kinon, Bruce J./AAJ-2889-2020
   Rabinowitz, Jonathan/Q-4799-2019
   },
ORCID-Numbers = {Rabinowitz, Jonathan/0000-0002-6845-8064
   Rabinowitz, Jonathan/0000-0002-6845-8064
   Opler, Lewis/0000-0002-4443-8675},
Funding-Acknowledgement = {Innovative Medicine Initiative Joint Undertaking {[}115008]; European
   Union},
Funding-Text = {The research leading to these results has received support from the
   Innovative Medicine Initiative Joint Undertaking under grant agreement
   no. 115008 of which resources are composed of European Federation of
   Pharmaceutical Industries and Associations (EFPIA) in-kind contribution
   and financial contribution from the European Union's Seventh Framework
   Programme (FP7/2007-2013). Funding source was not involved in the
   collection, analysis, and interpretation of data; in the writing of the
   report; and nor in the decision to submit the paper for publication.},
Number-of-Cited-References = {4},
Times-Cited = {9},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Schizophr. Res.},
Doc-Delivery-Number = {FO6OK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000416984300012},
OA = {Green Published, hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000504322300025,
Author = {Horn, Andreas and Wenzel, Gregor and Irmen, Friederike and Huebl, Julius
   and Li, Ningfei and Neumann, Wolf-Julian and Krause, Patricia and
   Bohner, Georg and Scheel, Michael and Kuehn, Andrea A.},
Title = {Deep brain stimulation induced normalization of the human functional
   connectome in Parkinson's disease},
Journal = {BRAIN},
Year = {2019},
Volume = {142},
Number = {10},
Pages = {3129-3143},
Month = {OCT},
Abstract = {Neuroimaging has seen a paradigm shift away from a formal description of
   local activity patterns towards studying distributed brain networks. The
   recently defined framework of the `human connectome' enables global
   analysis of parts of the brain and their interconnections. Deep brain
   stimulation (DBS) is an invasive therapy for patients with severe
   movement disorders aiming to retune abnormal brain network activity by
   local high frequency stimulation of the basal ganglia. Beyond clinical
   utility, DBS represents a powerful research platform to study functional
   connectomics and the modulation of distributed brain networks in the
   human brain. We acquired resting-state functional MRI in 20 patients
   with Parkinson's disease with subthalamic DBS switched on and off. An
   age-matched control cohort of 15 subjects was acquired from an open data
   repository. DBS lead placement in the subthalamic nucleus was localized
   using a state-of-the art pipeline that involved brain shift correction,
   multispectral image registration and use of a precise subcortical atlas.
   Based on a realistic 3D model of the electrode and surrounding anatomy,
   the amount of local impact of DBS was estimated using a finite element
   method approach. On a global level, average connectivity increases and
   decreases throughout the brain were estimated by contrasting on and off
   DBS scans on a voxel-wise graph comprising eight thousand nodes. Local
   impact of DBS on the motor subthalamic nucleus explained half the
   variance in global connectivity increases within the motor network (R =
   0.711, P < 0.001). Moreover, local impact of DBS on the motor
   subthalamic nucleus could explain the degree to how much voxel-wise
   average brain connectivity normalized towards healthy controls (R =
   0.713, P < 0.001). Finally, a network-based statistics analysis revealed
   that DBS attenuated specific couplings known to be pathological in
   Parkinson's disease. Namely, coupling between motor thalamus and motor
   cortex was increased while striatal coupling with cerebellum, external
   pallidum and subthalamic nucleus was decreased by DBS. Our results show
   that resting state functional MRI may be acquired in DBS on and off
   conditions on clinical MRI hardware and that data are useful to gain
   additional insight into how DBS modulates the functional connectome of
   the human brain. We demonstrate that effective DBS increases overall
   connectivity in the motor network, normalizes the network profile
   towards healthy controls and specifically strengthens thalamo-cortical
   connectivity while reducing striatal control over basal ganglia and
   cerebellar structures.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Horn, A (Corresponding Author), Charite Univ Med Berlin, Charitepl 1, D-10117 Berlin, Germany.
   Horn, Andreas; Wenzel, Gregor; Irmen, Friederike; Huebl, Julius; Li, Ningfei; Neumann, Wolf-Julian; Krause, Patricia; Kuehn, Andrea A., Charite Univ Med Berlin, Dept Neurol, Movement Disorders \& Neuromodulat Sect, Berlin, Germany.
   Irmen, Friederike; Kuehn, Andrea A., Humboldt Univ, Berlin Sch Mind \& Brain, Berlin, Germany.
   Neumann, Wolf-Julian; Bohner, Georg; Scheel, Michael, Charite Univ Med Berlin, Dept Neuroradiol, Berlin, Germany.
   Kuehn, Andrea A., Charite Univ Med Berlin, Exzellenzcluster NeuroCure, Berlin, Germany.},
DOI = {10.1093/brain/awz239},
ISSN = {0006-8950},
EISSN = {1460-2156},
Keywords = {Parkinson's disease; deep brain stimulation; network modulation;
   resting-state functional MRI; brain connectivity},
Keywords-Plus = {CONNECTIVITY; MRI; ORGANIZATION; PATTERNS; TOOLBOX; VOLUME; ATLAS;
   SEGMENTATION; ACTIVATION; CIRCUITS},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Clinical Neurology; Neurosciences},
Author-Email = {andreas.horn@charite.de},
Affiliations = {Free University of Berlin; Humboldt University of Berlin; Charite
   Universitatsmedizin Berlin; Humboldt University of Berlin; Free
   University of Berlin; Humboldt University of Berlin; Charite
   Universitatsmedizin Berlin; Free University of Berlin; Humboldt
   University of Berlin; Charite Universitatsmedizin Berlin},
ResearcherID-Numbers = {Neumann, med. Wolf-Julian/D-7131-2011
   Li, Ningfei/DUZ-2031-2022
   Horn, Andreas/R-6528-2017
   },
ORCID-Numbers = {Neumann, med. Wolf-Julian/0000-0002-6758-9708
   Li, Ningfei/0000-0003-3315-3591
   Horn, Andreas/0000-0002-0695-6025
   Irmen, Friederike/0000-0001-5574-3790
   Kuhn, Andrea A./0000-0002-4134-9060
   Bohner, Georg/0000-0002-1919-092X
   Scheel, Michael/0000-0002-3505-2914
   Krause, Patricia/0000-0001-9063-0556},
Funding-Acknowledgement = {DFG {[}SPP 2041]; DFG Emmy Noether grant {[}410169619]; Michael J. Fox
   Foundation for Parkinson's Research},
Funding-Text = {The study was supported by DFG grant SPP 2041 to A.A.K. and DFG Emmy
   Noether grant 410169619 to A.H. Data used in the preparation of this
   article were obtained from the Parkinson's Progression Markers
   Initiative (PPMI) database (www.ppmi-info.org/data).For up-to-date
   information on the study, visit www.ppmi-info.org.PPMI-a public-private
   partnership-is funded by the Michael J. Fox Foundation for Parkinson's
   Research and funding partners, see www.ppmi-info.org/fundingpartners.},
Number-of-Cited-References = {83},
Times-Cited = {77},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {18},
Journal-ISO = {Brain},
Doc-Delivery-Number = {JY3MJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000504322300025},
OA = {Green Submitted, Bronze},
DA = {2024-01-15},
}

@article{ WOS:000335370600004,
Author = {Rueegg, Janine and Gries, Corinna and Bond-Lamberty, Ben and Bowen,
   Gabriel J. and Felzer, Benjamin S. and McIntyre, Nancy E. and Soranno,
   Patricia A. and Vanderbilt, Kristin L. and Weathers, Kathleen C.},
Title = {Completing the data life cycle: using information management in
   macrosystems ecology research},
Journal = {FRONTIERS IN ECOLOGY AND THE ENVIRONMENT},
Year = {2014},
Volume = {12},
Number = {1},
Pages = {24-30},
Month = {FEB},
Abstract = {An important goal of macrosystems ecology (MSE) research is to advance
   understanding of ecological systems at both fine and broad temporal and
   spatial scales. Our premise in this paper is that MSE projects require
   integrated information management at their inception. Such efforts will
   lead to improved communication and sharing of knowledge among diverse
   project participants, better science outcomes, and more transparent and
   accessible (ie open) science. We encourage researchers to complete the
   data life cycle by publishing well-documented datasets, thereby
   facilitating re-use of the data to answer new and different questions
   from the ones conceived by those involved in the original projects. The
   practice of documenting and submitting datasets to data repositories
   that are publicly accessible ensures that research results and data are
   available to and use-able by other researchers, thus fostering open
   science. However, ecologists are often unfamiliar with the requirements
   and information management tools for effectively preserving data and
   receive little institutional or professional incentive to do so. Here,
   we provide recommendations for achieving these ends and give examples
   from current MSE projects to demonstrate why information management is
   critical for ensuring that scientific results can be reproduced and that
   data can be shared for future use.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Rüegg, J (Corresponding Author), Kansas State Univ, Div Biol, Ackert Hall, Manhattan, KS 66506 USA.
   Rueegg, Janine, Kansas State Univ, Div Biol, Manhattan, KS 66506 USA.
   Gries, Corinna, Univ Wisconsin, Ctr Limnol, Madison, WI 53706 USA.
   Bond-Lamberty, Ben, Pacific NW Natl Lab, JGCRI, College Pk, MD USA.
   Bowen, Gabriel J., Univ Utah, Dept Geol \& Geophys, Salt Lake City, UT 84112 USA.
   Bowen, Gabriel J., Univ Utah, Global Change \& Sustainabil Ctr, Salt Lake City, UT USA.
   Felzer, Benjamin S., Lehigh Univ, Dept Earth \& Environm Sci, Bethlehem, PA 18015 USA.
   McIntyre, Nancy E., Texas Tech Univ, Dept Biol Sci, Lubbock, TX 79409 USA.
   Soranno, Patricia A., Michigan State Univ, Dept Fisheries \& Wildlife, E Lansing, MI 48824 USA.
   Vanderbilt, Kristin L., Univ New Mexico, Dept Biol, Albuquerque, NM 87131 USA.
   Weathers, Kathleen C., Cary Inst Ecosyst Studies, Millbrook, NY USA.},
DOI = {10.1890/120375},
ISSN = {1540-9295},
EISSN = {1540-9309},
Keywords-Plus = {CONTERMINOUS UNITED-STATES; CARBON SEQUESTRATION; OZONE},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology; Environmental Sciences},
Author-Email = {jrueegg@ksu.edu},
Affiliations = {Kansas State University; University of Wisconsin System; University of
   Wisconsin Madison; United States Department of Energy (DOE); Pacific
   Northwest National Laboratory; Utah System of Higher Education;
   University of Utah; Utah System of Higher Education; University of Utah;
   Lehigh University; Texas Tech University System; Texas Tech University;
   Michigan State University; University of New Mexico; Cary Institute of
   Ecosystem Studies},
ResearcherID-Numbers = {Rüegg, Janine/AFP-1428-2022
   Bowen, Gabriel J/C-1708-2008
   Felzer, Benjamin S/AAB-3456-2021
   Bond-Lamberty, Benjamin/C-6058-2008
   },
ORCID-Numbers = {Rüegg, Janine/0000-0002-7090-4852
   Felzer, Benjamin S/0000-0002-3990-3739
   Bond-Lamberty, Benjamin/0000-0001-9525-4633
   Gries, Corinna/0000-0002-9091-6543
   Newman, Gregory/0000-0003-0503-5782
   McIntyre, Nancy/0000-0003-1790-3057
   Soranno, Patricia/0000-0003-1668-9271
   Vanderbilt, Kristin/0000-0003-1439-2204},
Funding-Acknowledgement = {MacroSystems Biology Program in the Emerging Frontiers Division of the
   Biological Sciences Directorate at NSF; Direct For Biological Sciences;
   Emerging Frontiers {[}1258503, 1065818, 1065786, 1241286, 1065255]
   Funding Source: National Science Foundation; Division Of Environmental
   Biology; Direct For Biological Sciences {[}1232294, 1440297] Funding
   Source: National Science Foundation},
Funding-Text = {We thank all participants at the NSF-MacroSystems Biology PI meeting in
   Boulder, CO (March 2012), for fruitful discussions that led to this
   Special Issue and this paper. In particular, J O'Neil-Dunne provided
   comments on the inception and outlines of this manuscript. We also thank
   H Gholz and L Blood (NSF) for helpful discussions, as well as the
   MacroSystems Biology Program in the Emerging Frontiers Division of the
   Biological Sciences Directorate at NSF for support. For author
   contributions, see WebPanel 2.},
Number-of-Cited-References = {35},
Times-Cited = {52},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {70},
Journal-ISO = {Front. Ecol. Environ.},
Doc-Delivery-Number = {AG4DX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000335370600004},
OA = {Green Submitted, Bronze},
DA = {2024-01-15},
}

@article{ WOS:000746566600001,
Author = {Pajdla, Petr and Trampota, Frantisek},
Title = {Neolithic Settlements in Central Europe: Data from the Project
   `Lifestyle as an Unintentional Identity in the Neolithic'},
Journal = {JOURNAL OF OPEN ARCHAEOLOGY DATA},
Year = {2021},
Volume = {9},
Pages = {1-6},
Month = {DEC 29},
Abstract = {This dataset comprises the core spatial and temporal structure of the
   `Lifestyle as an Unintentional Identity in the Neolithic' project. The
   data consist of spatial and chronological information on 2,154 Neolithic
   settlement sites from c. 4900 to 3300 BCE in two separate regions, the
   eastern part of Bohemia (Czech Republic) and the Morava River basin
   (Czech Republic, parts of Austria and Slovakia). To gather as much data
   as possible, all available sources including published works, find and
   excavation reports in archives, museum collections and unpublished
   records and both existing and legacy databases were examined. The
   dataset is deposited at the Zenodo data repository with an open access
   license. There is a reuse potential in aggregating the data with data
   from different regions and/or time periods for various spatial and
   temporal analyses.},
Publisher = {UBIQUITY PRESS LTD},
Address = {Unit 3.22, East London Works, 65-75 Whitechapel Road, LONDON, E1 1DU,
   ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Pajdla, P (Corresponding Author), Masaryk Univ, Dept Archaeol \& Museol, Brno, Czech Republic.
   Pajdla, Petr; Trampota, Frantisek, Masaryk Univ, Dept Archaeol \& Museol, Brno, Czech Republic.},
DOI = {10.5334/joad.882},
ISSN = {2049-1565},
Keywords = {Neolithic; Central Europe; settlement analysis; landscape; lithic raw
   materials; relative chronology},
Research-Areas = {Archaeology},
Web-of-Science-Categories  = {Archaeology},
Author-Email = {petr.pajdla@protonmail.com},
Affiliations = {Masaryk University Brno},
ResearcherID-Numbers = {Trampota, František/AAA-1338-2022
   Pajdla, Petr/GPG-4126-2022
   Trampota, František/AAA-4266-2022},
ORCID-Numbers = {Trampota, František/0000-0001-8437-9246
   Pajdla, Petr/0000-0001-7050-9572
   Trampota, František/0000-0001-8437-9246},
Funding-Acknowledgement = {Czech Science Foundation {[}19-16304S]},
Funding-Text = {The research described in this paper was conducted with support from the
   project `Lifestyle as an Unintentional Identity in the Neolithic'
   (Project 19-16304S), financed by the Czech Science Foundation.},
Number-of-Cited-References = {9},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {J. Open Archaeol. Data},
Doc-Delivery-Number = {YM4SR},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000746566600001},
DA = {2024-01-15},
}

@article{ WOS:000471246200001,
Author = {Porwollik, Vera and Rolinski, Susanne and Heinke, Jens and Mueller,
   Christoph},
Title = {Generating a rule-based global gridded tillage dataset},
Journal = {EARTH SYSTEM SCIENCE DATA},
Year = {2019},
Volume = {11},
Number = {2},
Pages = {823-843},
Month = {JUN 12},
Abstract = {Tillage is a central element in agricultural soil management and has
   direct and indirect effects on processes in the biosphere. Effects of
   agricultural soil management can be assessed by soil, crop, and
   ecosystem models, but global assessments are hampered by lack of
   information on the type of tillage and their spatial distribution. This
   study describes the generation of a classification of tillage practices
   and presents the spatially explicit mapping of these crop-specific
   tillage systems for around the year 2005.
   Tillage practices differ by the kind of equipment used, soil surface and
   depth affected, timing, and their purpose within the cropping systems.
   We classified the broad variety of globally relevant tillage practices
   into six categories: no-tillage in the context of Conservation
   Agriculture, traditional annual, traditional rotational, rotational,
   reduced, and conventional annual tillage. The identified tillage systems
   were allocated to gridded crop-specific cropland areas with a resolution
   of 5 arcmin. Allocation rules were based on literature findings and
   combine area information on crop type, water management regime, field
   size, water erosion, income, and aridity. We scaled reported national
   Conservation Agriculture areas down to grid cells via a
   probability-based approach for 54 countries. We provide area estimates
   of the six tillage systems aggregated to global and country scale. We
   found that 8.67Mkm(2) of global cropland area was tilled intensively at
   least once a year, whereas the remaining 2.65Mkm(2) was tilled less
   intensely. Further, we identified 4.67Mkm(2) of cropland as an area
   where Conservation Agriculture could be expanded to under current
   conditions.
   The tillage classification enables the parameterization of different
   soil management practices in various kinds of model simulations. The
   crop-specific tillage dataset indicates the spatial distribution of soil
   management practices, which is a prerequisite to assess erosion, carbon
   sequestration potential, as well as water, and nutrient dynamics of
   cropland soils. The dynamic definition of the allocation rules and
   accounting for national statistics, such as the share of Conservation
   Agriculture per country, also allow for derivation of datasets for
   historical and future global soil management scenarios. The resulting
   tillage system dataset and source code are accessible via an open-data
   repository (DOIs:https://doi.org/10.5880/PIK.2019.009 and
   https://doi.org/10.5880/PIK.2019.010, Porwollik et al., 2019a, b).},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Porwollik, V (Corresponding Author), Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany.
   Porwollik, Vera, Potsdam Inst Climate Impact Res, D-14412 Potsdam, Germany.
   Leibniz Assoc, D-14412 Potsdam, Germany.},
DOI = {10.5194/essd-11-823-2019},
ISSN = {1866-3508},
EISSN = {1866-3516},
Keywords-Plus = {CONSERVATION AGRICULTURE; LAND-USE; SOIL-EROSION; CLIMATE-CHANGE;
   MANAGEMENT; SYSTEMS; CROPLAND; YIELD; MODELS},
Research-Areas = {Geology; Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary; Meteorology \& Atmospheric Sciences},
Author-Email = {vera.porwollik@pik-potsdam.de},
Affiliations = {Potsdam Institut fur Klimafolgenforschung},
ResearcherID-Numbers = {Müller, Christoph/E-4812-2016
   },
ORCID-Numbers = {Müller, Christoph/0000-0002-9491-3550
   Porwollik, Vera/0000-0001-5866-8538},
Funding-Acknowledgement = {German Federal Ministry of Education and Research {[}01LN1317A,
   031B0170A]},
Funding-Text = {This research has been supported by the German Federal Ministry of
   Education and Research (grant nos. 01LN1317A and 031B0170A).},
Number-of-Cited-References = {73},
Times-Cited = {28},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {32},
Journal-ISO = {Earth Syst. Sci. Data},
Doc-Delivery-Number = {IC8QI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000471246200001},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000760358600010,
Author = {Eke, Damian O. and Bernard, Amy and Bjaalie, Jan G. and Chavarriaga,
   Ricardo and Hanakawa, Takashi and Hannan, Anthony J. and Hill, Sean L.
   and Martone, Maryann E. and McMahon, Agnes and Ruebel, Oliver and Crook,
   Sharon and Thiels, Edda and Pestilli, Franco},
Title = {International data governance for neuroscience},
Journal = {NEURON},
Year = {2022},
Volume = {110},
Number = {4},
Pages = {600-612},
Month = {FEB 16},
Abstract = {As neuroscience projects increase in scale and cross international
   borders, different ethical principles, national and international laws,
   regulations, and policies for data sharing must be considered. These
   concerns are part of what is collectively called data governance.
   Whereas neuroscience data transcend borders, data governance is
   typically constrained within geopolitical boundaries. An international
   data governance framework and accompanying infrastructure can assist
   investigators, institutions, data repositories, and funders with
   navigating disparate policies. Here, we propose principles and
   operational considerations for how data governance in neuroscience can
   be navigated at an international scale and highlight gaps, challenges,
   and opportunities in a global brain data ecosystem. We consider how to
   approach data governance in a way that balances data protection
   requirements and the need for open science, so as to promote
   international collaboration through federated constructs such as the
   International Brain Initiative (IBI).},
Publisher = {CELL PRESS},
Address = {50 HAMPSHIRE ST, FLOOR 5, CAMBRIDGE, MA 02139 USA},
Type = {Review},
Language = {English},
Affiliation = {Pestilli, F (Corresponding Author), Univ Texas Austin, Dept Psychol, Ctr Perceptual Syst, Ctr Theoret \& Computat Neurosci, Austin, TX 78712 USA.
   Pestilli, F (Corresponding Author), Univ Texas Austin, Inst Neurosci, Austin, TX 78712 USA.
   Eke, Damian O., De Montfort Univ, Ctr Comp \& Social Responsibil, Leicester, Leics, England.
   Eke, Damian O., Human Brain Project, Los Angeles, CA USA.
   Bernard, Amy; McMahon, Agnes, Kavli Fdn, Los Angeles, CA USA.
   Bjaalie, Jan G., Univ Oslo, Oslo, Norway.
   Chavarriaga, Ricardo, Zurich Univ Appl Sci, Sch Engn, Ctr Artificial Intelligence, Zurich, Switzerland.
   Hanakawa, Takashi, Kyoto Univ, Grad Sch Med, Kyoto, Japan.
   Hannan, Anthony J., Univ Melbourne, Florey Inst Neurosci \& Mental Hlth, Melbourne, Vic, Australia.
   Hill, Sean L., Krembil Ctr Neuroinformat, Ctr Addict \& Mental Hlth, Toronto, ON, Canada.
   Martone, Maryann E., Univ Calif San Diego, San Diego, CA 92103 USA.
   Ruebel, Oliver, Lawrence Berkeley Natl Lab, Sci Data Div, Berkeley, CA USA.
   Crook, Sharon, Arizona State Univ, Sch Math \& Stat Sci, Tempe, AZ USA.
   Thiels, Edda, Natl Sci Fdn, Alexandria, VA USA.
   Pestilli, Franco, Univ Texas Austin, Dept Psychol, Ctr Perceptual Syst, Ctr Theoret \& Computat Neurosci, Austin, TX 78712 USA.
   Pestilli, Franco, Univ Texas Austin, Inst Neurosci, Austin, TX 78712 USA.},
DOI = {10.1016/j.neuron.2021.11.017},
EarlyAccessDate = {FEB 2022},
ISSN = {0896-6273},
EISSN = {1097-4199},
Keywords-Plus = {BIG DATA; BRAIN PROJECT},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Neurosciences},
Author-Email = {pestilli@utexas.edu},
Affiliations = {De Montfort University; University of Oslo; Zurich University of Applied
   Sciences; Kyoto University; University of Melbourne; Florey Institute of
   Neuroscience \& Mental Health; University of Toronto; Centre for
   Addiction \& Mental Health - Canada; University of California System;
   University of California San Diego; United States Department of Energy
   (DOE); Lawrence Berkeley National Laboratory; Arizona State University;
   Arizona State University-Tempe; National Science Foundation (NSF);
   University of Texas System; University of Texas Austin; University of
   Texas System; University of Texas Austin},
ResearcherID-Numbers = {Chavarriaga, Ricardo/F-8952-2013
   Pestilli, Franco/J-5236-2012
   },
ORCID-Numbers = {Chavarriaga, Ricardo/0000-0002-8879-2860
   Pestilli, Franco/0000-0002-2469-0494
   Eke, Damian/0000-0002-6210-1283
   Hanakawa, Takashi/0000-0003-3267-8214
   Bjaalie, Jan G./0000-0001-7899-906X
   Bernard, Amy/0000-0003-2540-1153
   Hannan, Anthony/0000-0001-7532-8922
   McMahon, Agnes/0000-0002-1516-2462},
Funding-Acknowledgement = {Kavli Foundation; European Union's Horizon 2020 Framework Programme for
   Research and Innovation {[}945539]; National Institute of Neurological
   Disorders and Stroke of the NIH {[}U24NS120057]; National Health and
   Medical Research Council (NHMRC); DHB Foundation; Flicker of Hope
   Foundation; Krembil Foundation; Strategic International Brain Science
   Research Promotion Program {[}21dm0307003h0004, 21dm0307004h0003]; Brain
   Mapping by Integrated Neurotechnologies for Disease Studies from the
   Japan Agency for Medical Research and Development {[}21dm0207070h0001];
   NSF {[}IIS 1636893, IIS 1912270, BCS 1734853]; NIH National Institute of
   Biomedical Imaging and Bioengineering (NIBIB) {[}1R01EB029272]; NIH NIMH
   {[}1R01MH126699]; Microsoft Investigator Fellowship},
Funding-Text = {The authors' views are personal views and do not necessarily represent
   those of the organizations with which they are affiliated, such as the
   National Science Foundation (NSF) , National Institutes of Health (NIH)
   or US federal government. We thank Kenji Doya, Megumi Maruyama, and
   Nargis Akter for admin-istrative support. A.M. and A.B. are supported by
   the Kavli Foundation. D.O.E. and J.G.B. are supported by the European
   Union's Horizon 2020 Framework Programme for Research and Innovation
   under Specific Grant Agreement (SGA) 945539 (HBP, SGA3) . O.R. is
   supported by the National Institute of Neurological Disorders and Stroke
   of the NIH under award U24NS120057. A.J.H. is supported by a Principal
   Research Fellowship and Ideas Grant from the National Health and Medical
   Research Council (NHMRC) and by the DHB Foundation (Equity Trustees) and
   Flicker of Hope Foundation. S.L.H. is supported by Krembil Foundation
   funding. T.H. is supported by the Strategic International Brain Science
   Research Promotion Program (21dm0307003h0004 and 21dm0307004h0003) and
   Brain Mapping by Integrated Neurotechnologies for Disease Studies
   (21dm0207070h0001) from the Japan Agency for Medical Research and
   Development. F.P. is supported by NSF grants IIS 1636893, IIS 1912270,
   and BCS 1734853, NIH National Institute of Biomedical Imaging and
   Bioengineering (NIBIB) grant 1R01EB029272, NIH NIMH 1R01MH126699, and a
   Microsoft Investigator Fellowship.},
Number-of-Cited-References = {79},
Times-Cited = {18},
Usage-Count-Last-180-days = {16},
Usage-Count-Since-2013 = {50},
Journal-ISO = {Neuron},
Doc-Delivery-Number = {ZG6HV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000760358600010},
OA = {Green Submitted, hybrid, Green Published, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000968034400001,
Author = {Bona, Jonathan and Kemp, Aaron S. and Cox, Carli and Nolan, Tracy S. and
   Pillai, Lakshmi and Das, Aparna and Galvin, James E. and Larson-Prior,
   Linda and Virmani, Tuhin and Prior, Fred},
Title = {Semantic Integration of Multi-Modal Data and Derived Neuroimaging
   Results Using the Platform for Imaging in Precision Medicine (PRISM) in
   the Arkansas Imaging Enterprise System (ARIES)},
Journal = {FRONTIERS IN ARTIFICIAL INTELLIGENCE},
Year = {2022},
Volume = {4},
Month = {FEB 10},
Abstract = {Neuroimaging is among the most active research domains for the creation
   and management of open-access data repositories. Notably lacking from
   most data repositories are integrated capabilities for semantic
   representation. The Arkansas Imaging Enterprise System (ARIES) is a
   research data management system which features integrated capabilities
   to support semantic representations of multi-modal data from disparate
   sources (imaging, behavioral, or cognitive assessments), across common
   image-processing stages (preprocessing steps, segmentation schemes,
   analytic pipelines), as well as derived results (publishable findings).
   These unique capabilities ensure greater reproducibility of scientific
   findings across large-scale research projects. The current investigation
   was conducted with three collaborating teams who are using ARIES in a
   project focusing on neurodegeneration. Datasets included magnetic
   resonance imaging (MRI) data as well as non-imaging data obtained from a
   variety of assessments designed to measure neurocognitive functions
   (performance scores on neuropsychological tests). We integrate and
   manage these data with semantic representations based on axiomatically
   rich biomedical ontologies. These instantiate a knowledge graph that
   combines the data from the study cohorts into a shared semantic
   representation that explicitly accounts for relations among the entities
   that the data are about. This knowledge graph is stored in a
   triple-store database that supports reasoning over and querying these
   integrated data. Semantic integration of the non-imaging data using
   background information encoded in biomedical domain ontologies has
   served as a key feature-engineering step, allowing us to combine
   disparate data and apply analyses to explore associations, for instance,
   between hippocampal volumes and measures of cognitive functions derived
   from various assessment instruments.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Bona, J; Kemp, AS (Corresponding Author), Univ Arkansas Med Sci UAMS, Dept Biomed Informat, Little Rock, AR 72205 USA.
   Kemp, AS (Corresponding Author), Univ Arkansas Med Sci UAMS, Psychiat Res Inst, Neurocognit Dynam Lab, Little Rock, AR 72205 USA.
   Kemp, AS (Corresponding Author), Univ Arkansas Med Sci UAMS, Coll Med, Dept Psychiat, Little Rock, AR 72205 USA.
   Bona, Jonathan; Kemp, Aaron S.; Nolan, Tracy S.; Larson-Prior, Linda; Prior, Fred, Univ Arkansas Med Sci UAMS, Dept Biomed Informat, Little Rock, AR 72205 USA.
   Kemp, Aaron S.; Cox, Carli; Larson-Prior, Linda, Univ Arkansas Med Sci UAMS, Psychiat Res Inst, Neurocognit Dynam Lab, Little Rock, AR 72205 USA.
   Kemp, Aaron S.; Das, Aparna; Larson-Prior, Linda, Univ Arkansas Med Sci UAMS, Coll Med, Dept Psychiat, Little Rock, AR 72205 USA.
   Pillai, Lakshmi; Larson-Prior, Linda; Virmani, Tuhin, Univ Arkansas Med Sci UAMS, Coll Med, Dept Neurol, Little Rock, AR USA.
   Galvin, James E., Univ Miami, Comprehens Ctr Brain Hlth, Dept Neurol, Miller Sch Med, Miami, FL USA.
   Prior, Fred, Univ Arkansas Med Sci UAMS, Coll Med, Dept Radiol, Little Rock, AR USA.},
DOI = {10.3389/frai.2021.649970},
Article-Number = {649970},
EISSN = {2624-8212},
Keywords = {imaging informatics; knowledge representation; ontologies (artificial
   intelligence); semantic web; neuroinformatics},
Keywords-Plus = {PARKINSONS-DISEASE; ALZHEIMERS-DISEASE; PERFORMANCE; ONTOLOGIES;
   DEMENTIA},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Artificial Intelligence; Computer Science, Information
   Systems},
Author-Email = {jbona@uams.edu
   askemp@uams.edu},
Affiliations = {University of Arkansas System; University of Arkansas Medical Sciences;
   University of Arkansas System; University of Arkansas Medical Sciences;
   University of Arkansas System; University of Arkansas Medical Sciences;
   University of Arkansas System; University of Arkansas Medical Sciences;
   University of Miami; University of Arkansas System; University of
   Arkansas Medical Sciences},
ORCID-Numbers = {Pillai, Lakshmi/0000-0002-6570-2041
   Kemp, Aaron/0000-0001-6925-5667},
Funding-Acknowledgement = {National Cancer Institute; National Institutes of Health
   {[}HHSN261200800001E]; Leidos Biomedical Research {[}16X011]; UAMS
   Translational Research Institute (TRI) through the National Center for
   Advancing Translational Sciences of the National Institutes of Health
   (NIH) {[}UL1 TR003107]; Michael J. Fox Foundation for Parkinson's
   Research;  {[}U24CA215109]},
Funding-Text = {This project has been funded in whole or in part with federal funds from
   the National Cancer Institute, National Institutes of Health under
   Contract No. HHSN261200800001E. The content of this publication does not
   necessarily reflect the views or policies of the Department of Health
   and Human Services, nor does mention of trade names, commercial
   products, or organizations imply endorsement by the U.S. Government.
   Under this contract the University of Arkansas is funded by Leidos
   Biomedical Research subcontract 16X011. Funding was also provided by
   U24CA215109. This project is supported in part by the UAMS Translational
   Research Institute (TRI), grant UL1 TR003107 through the National Center
   for Advancing Translational Sciences of the National Institutes of
   Health (NIH). The content is solely the responsibility of the authors
   and does not necessarily represent the official views of the NIH.
   Additional support was provided by a competitive research grant (PI:
   Galvin) from the Michael J. Fox Foundation for Parkinson's Research,
   which had no direct involvement in the collection, analysis, or
   interpretation of the data presented herein. Data used in the
   preparation of this article were obtained from the Parkinson's
   Progression Markers Initiative (PPMI) database (www.ppmi-info.org/data).
   PPMI is a public-private partnership funded by the Michael J. Fox
   Foundation for Parkinson's Research and funding partners {[}a listing of
   all of the PPMI funding partners can be found at
   www.ppmi-info.org/fundingpartners].},
Number-of-Cited-References = {44},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Front. Artif. Intell.},
Doc-Delivery-Number = {D3VI1},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000968034400001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000721355500002,
Author = {Kearnes, Steven M. and Maser, Michael R. and Wleklinski, Michael and
   Kast, Anton and Doyle, Abigail G. and Dreher, Spencer D. and Hawkins,
   Joel M. and Jensen, Klavs F. and Coley, Connor W.},
Title = {The Open Reaction Database},
Journal = {JOURNAL OF THE AMERICAN CHEMICAL SOCIETY},
Year = {2021},
Volume = {143},
Number = {45},
Pages = {18820-18826},
Month = {NOV 17},
Abstract = {Chemical reaction data in journal articles, patents, and even electronic
   laboratory notebooks are currently stored in various formats, often
   unstructured, which presents a significant barrier to downstream
   applications, including the training of machine-learning models. We
   present the Open Reaction Database (ORD), an open-access schema and
   infrastructure for structuring and sharing organic reaction data,
   including a centralized data repository. The ORD schema supports
   conventional and emerging technologies, from benchtop reactions to
   automated high-throughput experiments and flow chemistry. The data,
   schema, supporting code, and web-based user interfaces are all publicly
   available on GitHub. Our vision is that a consistent data representation
   and infrastructure to support data sharing will enable downstream
   applications that will greatly improve the state of the art with respect
   to computer-aided synthesis planning, reaction prediction, and other
   predictive chemistry tasks.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Review},
Language = {English},
Affiliation = {Kearnes, SM (Corresponding Author), Relay Therapeut, Cambridge, MA 02139 USA.
   Coley, CW (Corresponding Author), MIT, Dept Chem Engn, Cambridge, MA 02139 USA.
   Coley, CW (Corresponding Author), MIT, Dept Elect Engn \& Comp Sci, Cambridge, MA 02139 USA.
   Kearnes, Steven M., Relay Therapeut, Cambridge, MA 02139 USA.
   Maser, Michael R., CALTECH, Div Chem \& Chem Engn, Pasadena, CA 91125 USA.
   Wleklinski, Michael; Dreher, Spencer D., Merck \& Co Inc, Chem Capabil Accelerating Therapeut, Kenilworth, NJ 07033 USA.
   Kast, Anton, Google LLC, Mountain View, CA 94043 USA.
   Doyle, Abigail G., Univ Calif Los Angeles, Dept Chem \& Biochem, Los Angeles, CA 90095 USA.
   Hawkins, Joel M., Pfizer Worldwide Res \& Dev, Chem Res \& Dev, Groton, CT 06340 USA.
   Jensen, Klavs F.; Coley, Connor W., MIT, Dept Chem Engn, Cambridge, MA 02139 USA.
   Coley, Connor W., MIT, Dept Elect Engn \& Comp Sci, Cambridge, MA 02139 USA.},
DOI = {10.1021/jacs.1c09820},
EarlyAccessDate = {NOV 2021},
ISSN = {0002-7863},
EISSN = {1520-5126},
Keywords-Plus = {CHEMISTRY INFORMER LIBRARIES; PREDICTION; SYSTEM},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary},
Author-Email = {skearnes@relaytx.com
   ccoley@mit.edu},
Affiliations = {California Institute of Technology; Merck \& Company; Google
   Incorporated; University of California System; University of California
   Los Angeles; Pfizer; Massachusetts Institute of Technology (MIT);
   Massachusetts Institute of Technology (MIT)},
ResearcherID-Numbers = {Doyle, Abigail/JOK-9641-2023
   Jensen, Klavs F/F-2462-2012
   },
ORCID-Numbers = {Jensen, Klavs F/0000-0001-7192-580X
   /0000-0002-8271-8723
   Doyle, Abigail/0000-0002-6641-0833},
Funding-Acknowledgement = {Google; Relay Therapeutics},
Funding-Text = {There are many people to thank for help in getting this initiative
   started: all of the respondents to our original use case survey in 2019,
   the full advisory board, and all of the direct contributors to ord-data.
   We also thank Nathan Kim for helping with infrastructure development,
   Brian Lee for helping with feedback and beta testing, and Devin Sandberg
   and Zan Armstrong for design advice. Cloud computing resources and legal
   support were provided by Google. S.M.K. acknowledges support from Google
   and Relay Therapeutics. Additional GitHub data storage and bandwidth
   were provided through the GitHub Education program.},
Number-of-Cited-References = {28},
Times-Cited = {79},
Usage-Count-Last-180-days = {12},
Usage-Count-Since-2013 = {88},
Journal-ISO = {J. Am. Chem. Soc.},
Doc-Delivery-Number = {XB5FQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000721355500002},
OA = {hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000901864100001,
Author = {Ni, Zhixu and Wolk, Michele and Jukes, Geoff and Espinosa, Karla
   Mendivelso and Ahrends, Robert and Aimo, Lucila and Alvarez-Jarreta,
   Jorge and Andrews, Simon and Andrews, Robert and Bridge, Alan and Clair,
   Geremy C. and Conroy, Matthew J. and Fahy, Eoin and Gaud, Caroline and
   Goracci, Laura and Hartler, Juergen and Hoffmann, Nils and Kopczyinki,
   Dominik and Korf, Ansgar and Lopez-Clavijo, Andrea F. and Malik, Adnan
   and Ackerman, Jacobo Miranda and Molenaar, Martijn R. and O'Donovan,
   Claire and Pluskal, Tomas and Shevchenko, Andrej and Slenter, Denise and
   Siuzdak, Gary and Kutmon, Martina and Tsugawa, Hiroshi and Willighagen,
   Egon L. and Xia, Jianguo and O'Donnell, Valerie B. and Fedorova, Maria},
Title = {Guiding the choice of informatics software and tools for lipidomics
   research applications},
Journal = {NATURE METHODS},
Year = {2023},
Volume = {20},
Number = {2},
Pages = {193-204},
Month = {FEB},
Abstract = {Progress in mass spectrometry lipidomics has led to a rapid
   proliferation of studies across biology and biomedicine. These generate
   extremely large raw datasets requiring sophisticated solutions to
   support automated data processing. To address this, numerous software
   tools have been developed and tailored for specific tasks. However, for
   researchers, deciding which approach best suits their application relies
   on ad hoc testing, which is inefficient and time consuming. Here we
   first review the data processing pipeline, summarizing the scope of
   available tools. Next, to support researchers, LIPID MAPS provides an
   interactive online portal listing open-access tools with a graphical
   user interface. This guides users towards appropriate solutions within
   major areas in data processing, including (1) lipid-oriented databases,
   (2) mass spectrometry data repositories, (3) analysis of targeted
   lipidomics datasets, (4) lipid identification and (5) quantification
   from untargeted lipidomics datasets, (6) statistical analysis and
   visualization, and (7) data integration solutions. Detailed descriptions
   of functions and requirements are provided to guide customized data
   analysis workflows.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Fedorova, M (Corresponding Author), Fac Med Carl Gustav Carus TU Dresden, Ctr Membrane Biochem \& Lipid Res, Dresden, Germany.
   O'Donnell, VB (Corresponding Author), Cardiff Univ, Sch Med, Syst Immun Res Inst, Cardiff, Wales.
   Ni, Zhixu; Wolk, Michele; Fedorova, Maria, Fac Med Carl Gustav Carus TU Dresden, Ctr Membrane Biochem \& Lipid Res, Dresden, Germany.
   Jukes, Geoff; Espinosa, Karla Mendivelso; Alvarez-Jarreta, Jorge; Andrews, Robert; Conroy, Matthew J.; O'Donnell, Valerie B., Cardiff Univ, Sch Med, Syst Immun Res Inst, Cardiff, Wales.
   Ahrends, Robert; Kopczyinki, Dominik, Univ Vienna, Dept Analyt Chem, Vienna, Austria.
   Aimo, Lucila; Bridge, Alan, Ctr Med Univ Geneva, SIB Swiss Inst Bioinformat, Swiss Prot Grp, Geneva, Switzerland.
   Alvarez-Jarreta, Jorge; Malik, Adnan; O'Donovan, Claire, European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Hinxton, England.
   Andrews, Simon; Gaud, Caroline; Lopez-Clavijo, Andrea F., Babraham Inst, Babraham Res Campus, Cambridge, England.
   Clair, Geremy C., Pacific Northwest Natl Lab, Biol Sci Div, Richland, WA USA.
   Fahy, Eoin, Univ Calif San Diego, Dept Bioengn, San Diego, CA 92103 USA.
   Goracci, Laura, Univ Perugia, Dept Chem Biol \& Biotechnol, Perugia, Italy.
   Hartler, Juergen, Karl Franzens Univ Graz, Inst Pharmaceut Sci, Graz, Austria.
   Hartler, Juergen, Karl Franzens Univ Graz, Field Excellence BioHealthe, Graz, Austria.
   Hoffmann, Nils, Univ Bielefeld, Ctr Biotechnol, Bielefeld, Germany.
   Korf, Ansgar, Bruker Dalton GmbH \& Co KG, Bremen, Germany.
   Ackerman, Jacobo Miranda; Shevchenko, Andrej, Max Planck Inst Mol Cell Biol \& Genet, Dresden, Germany.
   Molenaar, Martijn R., European Mol Biol Lab, Struct \& Computat Biol Unit, Heidelberg, Germany.
   Pluskal, Tomas, Czech Acad Sci, Inst Organ Chem \& Biochem, Prague, Czech Republic.
   Slenter, Denise; Kutmon, Martina; Willighagen, Egon L., Maastricht Univ, Dept Bioinformat BiGCaT, NUTRIM, Maastricht, Netherlands.
   Siuzdak, Gary, Scripps Res Inst, Scripps Ctr Metabol \& Mass Spectrometry, La Jolla, CA USA.
   Kutmon, Martina, Maastricht Univ, Maastricht Ctr Syst Biol, Maastricht, Netherlands.
   Tsugawa, Hiroshi, Tokyo Univ Agr \& Technol, Dept Biotechnol \& Life Sci, Tokyo, Japan.
   Tsugawa, Hiroshi, RIKEN Ctr Sustainable Resource Sci, Yokohama, Kanagawa, Japan.
   Tsugawa, Hiroshi, RIKEN Ctr Integrat Med Sci, Yokohama, Kanagawa, Japan.
   Tsugawa, Hiroshi, Yokohama City Univ, Grad Sch Med Life Sci, Yokohama, Kanagawa, Japan.
   Xia, Jianguo, McGill Univ, Inst Parasitol, Montreal, PQ, Canada.},
DOI = {10.1038/s41592-022-01710-0},
EarlyAccessDate = {DEC 2022},
ISSN = {1548-7091},
EISSN = {1548-7105},
Keywords-Plus = {LC-MS; IDENTIFICATION; KNOWLEDGEBASE; SPHINGOLIPIDS; ANNOTATION;
   METABOLITE; LIPIDS; SEX},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods},
Author-Email = {O-DonnellVB@cardiff.ac.uk
   maria.fedorova@tu-dresden.de},
Affiliations = {Technische Universitat Dresden; Cardiff University; University of
   Vienna; Swiss Institute of Bioinformatics; University of Geneva;
   European Molecular Biology Laboratory (EMBL); UK Research \& Innovation
   (UKRI); Biotechnology and Biological Sciences Research Council (BBSRC);
   Babraham Institute; United States Department of Energy (DOE); Pacific
   Northwest National Laboratory; University of California System;
   University of California San Diego; University of Perugia; University of
   Graz; University of Graz; University of Bielefeld; Bruker Corporation;
   Bruker Daltonik GmbH; Max Planck Society; European Molecular Biology
   Laboratory (EMBL); Czech Academy of Sciences; Institute of Organic
   Chemistry \& Biochemistry of the Czech Academy of Sciences; Maastricht
   University; Scripps Research Institute; Maastricht University; Tokyo
   University of Agriculture \& Technology; RIKEN; RIKEN; Yokohama City
   University; McGill University},
ResearcherID-Numbers = {Ni, Zhixu/J-2041-2016
   Pluskal, Tomáš/C-6247-2012
   Clair, Geremy/L-3791-2018
   Slenter, Denise/JHT-4382-2023
   Kutmon, Martina/AAT-2718-2021
   Malik, Dr. Adnan/AAE-4914-2022
   Tsugawa, Hiroshi/HMV-9455-2023
   Goracci, Laura/G-3974-2014
   Ahrends, Robert/ISS-2350-2023
   O'Donnell, Valerie/C-6948-2012
   Bridge, Alan/U-4209-2018
   },
ORCID-Numbers = {Ni, Zhixu/0000-0003-3662-2621
   Pluskal, Tomáš/0000-0002-6940-3006
   Clair, Geremy/0000-0003-0478-8520
   Kutmon, Martina/0000-0002-7699-8191
   Tsugawa, Hiroshi/0000-0002-2015-3958
   Goracci, Laura/0000-0002-9282-9013
   Ahrends, Robert/0000-0003-0232-3375
   Aimo, Lucila/0000-0003-0943-6401
   Kopczynski, Dominik/0000-0001-5885-4568
   O'Donovan, Claire/0000-0001-8051-7429
   Hoffmann, Nils/0000-0002-6540-6875
   Wolk, Michele/0000-0001-5558-4582
   Willighagen, Egon/0000-0001-7542-0286
   Conroy, Matthew/0000-0001-7297-9623
   Bridge, Alan/0000-0003-2148-9135
   Fedorova, Maria/0000-0002-4692-3885
   Andrews, Simon/0000-0002-5006-3507},
Funding-Acknowledgement = {COST (European Cooperation in Science and Technology) {[}CA19105];
   Wellcome Trust {[}203014/Z/16/Z]; Cayman Chemical; Merck; Czech Science
   Foundation {[}21-11563M]; FWF {[}P33298-B]; Human Frontiers Science
   Progam {[}RGP0002/2022]; `Sonderzuweisung zur Unterstutzung
   profilbestimmender Struktureinheiten 2021' by the SMWK; Deutsche
   Forschungsgemeinschaft {[}FE 1236/5-1]; JSPS KAKENHI {[}21K18216];
   National Cancer Center Research and Development Fund {[}2020-A-9]; AMED
   Japan Program for Infectious Diseases Research and Infrastructure
   {[}21wm0325036h0001]; JST National Bioscience Database Center (NBDC);
   JST ERATO `Arita Lipidome Atlas Project' {[}JPMJER2101]; Austrian
   Science Fund (FWF) {[}P33298] Funding Source: Austrian Science Fund
   (FWF); Wellcome Trust {[}203014/Z/16/Z] Funding Source: Wellcome Trust},
Funding-Text = {This publication is based upon work from COST Action EpiLipidNET,
   Pan-European Network in Lipidomics and Epilipidomics (CA19105;
   https://www.epilipid.net), supported by COST (European Cooperation in
   Science and Technology). Funding from the Wellcome Trust is gratefully
   acknowledged for LIPID MAPS (203014/Z/16/Z). LIPID MAPS is grateful for
   sponsorship from Cayman Chemical, Merck and Avanti Polar Lipids. T.P. is
   supported by the Czech Science Foundation Grant 21-11563M. Funding from
   the FWF P33298-B and Human Frontiers Science Progam RGP0002/2022 is
   gratefully acknowledged. `Sonderzuweisung zur Unterstutzung
   profilbestimmender Struktureinheiten 2021' by the SMWK and Deutsche
   Forschungsgemeinschaft (FE 1236/5-1 to M.F.) are gratefully
   acknowledged. JSPS KAKENHI (21K18216 to H.T.), the National Cancer
   Center Research and Development Fund (2020-A-9, H.T.), AMED Japan
   Program for Infectious Diseases Research and Infrastructure
   (21wm0325036h0001 to H.T.), JST National Bioscience Database Center
   (NBDC to H.T.), JST ERATO `Arita Lipidome Atlas Project' (JPMJER2101 to
   H.T.).},
Number-of-Cited-References = {87},
Times-Cited = {15},
Usage-Count-Last-180-days = {11},
Usage-Count-Since-2013 = {26},
Journal-ISO = {Nat. Methods},
Doc-Delivery-Number = {I4KY1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000901864100001},
OA = {Bronze, Green Accepted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000622998100002,
Author = {Schmied, Hannes Mueller and Caceres, Denise and Eisner, Stephanie and
   Floerke, Martina and Herbert, Claudia and Niemann, Christoph and Peiris,
   Thedini Asali and Popat, Eklavyya and Portmann, Felix Theodor and
   Reinecke, Robert and Schumacher, Maike and Shadkam, Somayeh and Telteu,
   Camelia-Eliza and Trautmann, Tim and Doell, Petra},
Title = {The global water resources and use model WaterGAP v2.2d: model
   description and evaluation},
Journal = {GEOSCIENTIFIC MODEL DEVELOPMENT},
Year = {2021},
Volume = {14},
Number = {2},
Pages = {1037-1079},
Month = {FEB 23},
Abstract = {WaterGAP is a global hydrological model that quantifies human use of
   groundwater and surface water as well as water flows and water storage
   and thus water resources on all land areas of the Earth. Since 1996, it
   has served to assess water resources and water stress both historically
   and in the future, in particular under climate change. It has improved
   our understanding of continental water storage variations, with a focus
   on overexploitation and depletion of water resources. In this paper, we
   describe the most recent model version WaterGAP 2.2d, including the
   water use models, the linking model that computes net abstractions from
   groundwater and surface water and the WaterGAP Global Hydrology Model
   (WGHM). Standard model output variables that are freely available at a
   data repository are explained. In addition, the most requested model
   outputs, total water storage anomalies, streamflow and water use, are
   evaluated against observation data. Finally, we show examples of
   assessments of the global freshwater system that can be achieved with
   WaterGAP 2.2d model output.},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Schmied, HM (Corresponding Author), Goethe Univ Frankfurt, Inst Phys Geog, Frankfurt, Germany.
   Schmied, HM (Corresponding Author), Senckenberg Leibniz Biodivers \& Climate Res Ctr S, Frankfurt, Germany.
   Schmied, Hannes Mueller; Caceres, Denise; Herbert, Claudia; Niemann, Christoph; Peiris, Thedini Asali; Popat, Eklavyya; Portmann, Felix Theodor; Reinecke, Robert; Shadkam, Somayeh; Telteu, Camelia-Eliza; Trautmann, Tim; Doell, Petra, Goethe Univ Frankfurt, Inst Phys Geog, Frankfurt, Germany.
   Schmied, Hannes Mueller; Doell, Petra, Senckenberg Leibniz Biodivers \& Climate Res Ctr S, Frankfurt, Germany.
   Eisner, Stephanie, Norwegian Inst Bioecon Res NIBIO, As, Norway.
   Floerke, Martina, Ruhr Univ Bochum, Engn Hydrol \& Water Resources Management, Bochum, Germany.
   Reinecke, Robert, Fed Inst Hydrol, Unt Ctr Water Resources \& Global Change UNESCO, Koblenz, Germany.
   Schumacher, Maike, Univ Hohenheim, Inst Phys \& Meteorol, Stuttgart, Germany.
   Schumacher, Maike, Univ Hohenheim, Computat Sci Lab CSL, Stuttgart, Germany.},
DOI = {10.5194/gmd-14-1037-2021},
ISSN = {1991-959X},
EISSN = {1991-9603},
Keywords-Plus = {CLIMATE-CHANGE; GROUNDWATER MODEL; VEGETATION MODEL; RIVER DISCHARGE;
   SCALE ANALYSIS; MANAGED LAND; GRACE DATA; DATA SET; ASSIMILATION;
   UNCERTAINTY},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {hannes.mueller.schmied@em.uni-frankfurt.de},
Affiliations = {Goethe University Frankfurt; Norwegian Institute of Bioeconomy Research;
   Ruhr University Bochum; University Hohenheim; University Hohenheim},
ResearcherID-Numbers = {Döll, Petra/A-3784-2009
   Schmied, Hannes Müller/K-6231-2013
   Reinecke, Robert/K-3693-2019
   },
ORCID-Numbers = {Döll, Petra/0000-0003-2238-4546
   Schmied, Hannes Müller/0000-0001-5330-9923
   Reinecke, Robert/0000-0001-5699-8584
   Floerke, Martina/0000-0003-2943-5289
   Eisner, Stephanie/0000-0002-0157-1636
   Caceres, Denise/0000-0003-3277-0694
   Popat, Eklavyya/0000-0002-3064-163X
   Ardhige, Thedini Asali Peiris/0000-0001-9071-6712},
Funding-Acknowledgement = {Open Access Fund of the Leibniz Association},
Funding-Text = {The publication of this article was funded by the Open Access Fund of
   the Leibniz Association.},
Number-of-Cited-References = {125},
Times-Cited = {112},
Usage-Count-Last-180-days = {34},
Usage-Count-Since-2013 = {151},
Journal-ISO = {Geosci. Model Dev.},
Doc-Delivery-Number = {QO2TJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000622998100002},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000619170500001,
Author = {McConnell, Brian},
Title = {The interstellar communication relay},
Journal = {INTERNATIONAL JOURNAL OF ASTROBIOLOGY},
Year = {2020},
Volume = {19},
Number = {6},
Pages = {419-422},
Month = {DEC},
Abstract = {The paper describes the architecture for a data repository and
   distribution system to be used in the case of a SETI detection event.
   This system is conceptually modelled after the Deep Space Network,
   although the hardware and infrastructure involved are different and
   substantially less expensive to operate. The system is designed to
   accommodate a large number of users from a variety of fields who wish to
   contribute to the analysis and comprehension effort that would follow
   the detection of an information-bearing signal.},
Publisher = {CAMBRIDGE UNIV PRESS},
Address = {32 AVENUE OF THE AMERICAS, NEW YORK, NY 10013-2473 USA},
Type = {Article},
Language = {English},
Affiliation = {McConnell, B (Corresponding Author), SETI Open Data Arch, San Francisco, CA 94107 USA.
   McConnell, Brian, SETI Open Data Arch, San Francisco, CA 94107 USA.},
DOI = {10.1017/S1473550420000178},
ISSN = {1473-5504},
EISSN = {1475-3006},
Keywords = {Information theory; interstellar; communication; meti; seti},
Research-Areas = {Astronomy \& Astrophysics; Life Sciences \& Biomedicine - Other Topics;
   Geology},
Web-of-Science-Categories  = {Astronomy \& Astrophysics; Biology; Geosciences, Multidisciplinary},
Author-Email = {bsmcconnell@gmail.com},
ORCID-Numbers = {McConnell, Brian/0000-0003-3373-9082},
Number-of-Cited-References = {7},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Int. J. Astrobiol.},
Doc-Delivery-Number = {QI7NP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000619170500001},
DA = {2024-01-15},
}

@article{ WOS:000475901600007,
Author = {Zagidullin, Bulat and Aldahdooh, Jehad and Zheng, Shuyu and Wang, Wenyu
   and Wang, Yinyin and Saad, Joseph and Malyutina, Alina and Jafari,
   Mohieddin and Tanoli, Ziaurrehman and Pessia, Alberto and Tang, Jing},
Title = {DrugComb: an integrative cancer drug combination data portal},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2019},
Volume = {47},
Number = {W1},
Pages = {W43-W51},
Month = {JUL 2},
Abstract = {Drug combination therapy has the potential to enhance efficacy, reduce
   dose-dependent toxicity and prevent the emergence of drug resistance.
   However, discovery of synergistic and effective drug combinations has
   been a laborious and often serendipitous process. In recent years,
   identification of combination therapies has been accelerated due to the
   advances in high-throughput drug screening, but informatics approaches
   for systems-level data management and analysis are needed. To contribute
   toward this goal, we created an open-access data portal called DrugComb
   (https://drugcomb.fimm.fi) where the results of drug combination
   screening studies are accumulated, standardized and harmonized. Through
   the data portal, we provided a web server to analyze and visualize
   users' own drug combination screening data. The users can also
   effectively participate a crowdsourcing data curation effect by
   depositing their data at DrugComb. To initiate the data repository, we
   collected 437 932 drug combinations tested on a variety of cancer cell
   lines. We showed that linear regression approaches, when considering
   chemical fingerprints as predictors, have the potential to achieve high
   accuracy of predicting the sensitivity of drug combinations. All the
   data and informatics tools are freely available in DrugComb to enable a
   more efficient utilization of data resources for future drug combination
   discovery.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Tang, J (Corresponding Author), Univ Helsinki, Inst Mol Med Finland, Helsinki Life Sci Inst, Helsinki, Finland.
   Tang, J (Corresponding Author), Univ Helsinki, Res Program Syst Oncol, Fac Med, Helsinki, Finland.
   Zagidullin, Bulat; Aldahdooh, Jehad; Zheng, Shuyu; Wang, Wenyu; Wang, Yinyin; Saad, Joseph; Malyutina, Alina; Jafari, Mohieddin; Tanoli, Ziaurrehman; Pessia, Alberto; Tang, Jing, Univ Helsinki, Inst Mol Med Finland, Helsinki Life Sci Inst, Helsinki, Finland.
   Tang, Jing, Univ Helsinki, Res Program Syst Oncol, Fac Med, Helsinki, Finland.},
DOI = {10.1093/nar/gkz337},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {SYNERGY; SCREEN; IDENTIFY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {jing.tang@helsinki.fi},
Affiliations = {University of Helsinki; University of Helsinki},
ResearcherID-Numbers = {Jafari, Mohieddin/M-2755-2019
   Zagidullin, Bulat/GPX-1131-2022
   Wang, Yin/HCI-9352-2022
   tang, jing/HHR-9815-2022
   Aldahdooh, Jehad/AAJ-9026-2021
   Jafari, Mohieddin/HOH-9652-2023
   Tang, Jing/W-1764-2019
   Tang, Jing/H-4084-2012
   Pessia, Alberto/N-3072-2014
   Zheng, Shuyu/AAH-2648-2021
   },
ORCID-Numbers = {Jafari, Mohieddin/0000-0002-6991-8587
   Aldahdooh, Jehad/0000-0002-9947-4067
   Jafari, Mohieddin/0000-0002-6991-8587
   Tang, Jing/0000-0001-7480-7710
   Tang, Jing/0000-0001-7480-7710
   Pessia, Alberto/0000-0001-8607-9191
   Zheng, Shuyu/0000-0003-0624-8077
   Tanoli, Ziaurrehman/0000-0003-2435-9862
   Saad, Joseph/0000-0001-7701-0328
   Zagidullin, Bulat/0000-0002-8386-110X},
Funding-Acknowledgement = {European Research Council (ERC) starting grant Drug-Comb (Informatics
   approaches for the rationale selection of personalized cancer drug
   combinations) {[}716063]; European Commission {[}824087]; Academy of
   Finland {[}317680]; China Scholarship Council {[}201706740080]; European
   Research Council (ERC) starting grant agreement DrugComb {[}716063];
   Finland's EDUFI Fellowship {[}TM-18-10928]},
Funding-Text = {European Research Council (ERC) starting grant Drug-Comb (Informatics
   approaches for the rationale selection of personalized cancer drug
   combinations) {[}No. 716063]; European Commission H2020 EOSC-life
   (Providing an open collaborative space for digital biology in Europe
   {[}No. 824087]; Academy of Finland Research Fellow grant {[}No. 317680];
   China Scholarship Council grant {[}No. 201706740080]; Finland's EDUFI
   Fellowship {[}No. TM-18-10928]. Funding for open access charge: European
   Research Council (ERC) starting grant agreement DrugComb {[}No. 716063].},
Number-of-Cited-References = {43},
Times-Cited = {99},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {26},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {IJ4VI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000475901600007},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000396575500003,
Author = {Zhang, Zhang and Zhao, Wenming and Xiao, Jingfa and Song, Shuhui and
   Hao, Lili and Li, Rujiao and Ma, Lina and Sheng, Xin and Sang, Jian and
   Wang, Yanqing and Tang, Bixia and Zhang, Zhewen and BIG Data Ctr Members},
Title = {The BIG Data Center: from deposition to integration to translation},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2017},
Volume = {45},
Number = {D1},
Pages = {D18-D24},
Month = {JAN 4},
Abstract = {Biological data are generated at unprecedentedly exponential rates,
   posing considerable challenges in big data deposition, integration and
   translation. The BIG Data Center, established at Beijing Institute of
   Genomics (BIG), Chinese Academy of Sciences, provides a suite of
   database resources, including (i) Genome Sequence Archive, a data
   repository specialized for archiving raw sequence reads, (ii) Gene
   Expression Nebulas, a data portal of gene expression profiles based
   entirely on RNA-Seq data, (iii) Genome Variation Map, a comprehensive
   collection of genome variations for featured species, (iv) Genome
   Warehouse, a centralized resource housing genome-scale data with
   particular focus on economically important animals and plants, (v)
   Methylation Bank, an integrated database of whole-genome single-base
   resolution methylomes and (vi) Science Wikis, a central access point for
   biological wikis developed for community annotations. The BIG Data
   Center is dedicated to constructing and maintaining biological databases
   through big data integration and value-added curation, conducting basic
   research to translate big data into big knowledge and providing freely
   open access to a variety of data resources in support of worldwide
   research activities in both academia and industry. All of these
   resources are publicly available and can be found at
   http://bigd.big.ac.cn.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Zhang, Z; Zhao, WM; Xiao, JF (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Zhang, Z; Xiao, JF (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Z; Xiao, JF (Corresponding Author), Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Song, Shuhui; Hao, Lili; Li, Rujiao; Ma, Lina; Sheng, Xin; Sang, Jian; Wang, Yanqing; Tang, Bixia; Zhang, Zhewen, Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Zhang, Zhang; Xiao, Jingfa; Hao, Lili; Ma, Lina; Sheng, Xin; Sang, Jian; Zhang, Zhewen, Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Zhang; Xiao, Jingfa; Sheng, Xin; Sang, Jian; Tang, Bixia, Univ Chinese Acad Sci, Beijing 100049, Peoples R China.},
DOI = {10.1093/nar/gkw1060},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {COMMUNITY CURATION; GENOME SEQUENCE; DRAFT SEQUENCE; RICE; REVEALS;
   KNOWLEDGE; DOG},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {zhangzhang@big.ac.cn
   zhaowm@big.ac.cn
   xiaojingfa@big.ac.cn},
Affiliations = {Chinese Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese
   Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese Academy
   of Sciences; University of Chinese Academy of Sciences, CAS},
ResearcherID-Numbers = {Ma, Lina/AAD-2435-2019
   Yu, Chunlei/AAI-1802-2021
   wang, yanqing/C-5680-2014
   song, shuhui/D-6015-2014
   Wang, Guangyu/AAM-5940-2021
   Zhang, Zhang/JAX-2097-2023
   Sun, Shixiang/GQA-4872-2022
   xiao, jing/HRB-7391-2023
   zhang, zhang/GQZ-6804-2022
   zhang, zheng/HCH-9684-2022
   tian, dongmei/HIR-8892-2022
   },
ORCID-Numbers = {wang, yanqing/0000-0002-3054-3079
   Wang, Guangyu/0000-0003-4803-7200
   Sun, Shixiang/0000-0001-5499-2963
   tian, dongmei/0000-0003-0564-625X
   Wu, Shuangyang/0000-0001-6305-3204
   Ma, Lina/0000-0001-6390-6289},
Funding-Acknowledgement = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDB13040500, XDA08020102]; National Key Research Program of China
   {[}2016YFC0901603, 2016YFB0201702, 2016YFC0901903]; National Programs
   for High Technology Research and Development {[}863 Program]
   {[}2015AA020108]; National Natural Science Foundation of China
   {[}31100915, 31200978, 31271386, 31471248]; International Partnership
   Program of the Chinese Academy of Sciences {[}153F11KYSB20160008]; Key
   Program of the Chinese Academy of Sciences {[}KJZD-EW-L14]; Key
   Technology Talent Program of the Chinese Academy of Sciences; 100 Talent
   Program of the Chinese Academy of Sciences},
Funding-Text = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDB13040500 to W.Z, Z.Z.; XDA08020102 to Z.Z.]; National Key Research
   Program of China {[}2016YFC0901603 to W.Z.; 2016YFB0201702,
   2016YFC0901903 to J.X.]; National Programs for High Technology Research
   and Development {[}863 Program; 2015AA020108 to Z.Z.]; National Natural
   Science Foundation of China {[}31100915 to L.H.; 31200978 to L.M.;
   31271386, 31471248 to J.X.]; International Partnership Program of the
   Chinese Academy of Sciences {[}153F11KYSB20160008]; Key Program of the
   Chinese Academy of Sciences {[}KJZD-EW-L14 to J.X.]; Key Technology
   Talent Program of the Chinese Academy of Sciences (to W.Z.); The 100
   Talent Program of the Chinese Academy of Sciences (to Z.Z.). Funding for
   open access charge: Strategic Priority Research Program of the Chinese
   Academy of Sciences.},
Number-of-Cited-References = {48},
Times-Cited = {93},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {52},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {EO3DQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000396575500003},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000371218400011,
Author = {Van Tuyl, Steven and Whitmire, Amanda L.},
Title = {Water, Water, Everywhere: Defining and Assessing Data Sharing in
   Academia},
Journal = {PLOS ONE},
Year = {2016},
Volume = {11},
Number = {2},
Month = {FEB 17},
Abstract = {Sharing of research data has begun to gain traction in many areas of the
   sciences in the past few years because of changing expectations from the
   scientific community, funding agencies, and academic journals. National
   Science Foundation (NSF) requirements for a data management plan (DMP)
   went into effect in 2011, with the intent of facilitating the
   dissemination and sharing of research results. Many projects that were
   funded during 2011 and 2012 should now have implemented the elements of
   the data management plans required for their grant proposals. In this
   paper we define `data sharing' and present a protocol for assessing
   whether data have been shared and how effective the sharing was. We then
   evaluate the data sharing practices of researchers funded by the NSF at
   Oregon State University in two ways: by attempting to discover
   project-level research data using the associated DMP as a starting
   point, and by examining data sharing associated with journal articles
   that acknowledge NSF support. Sharing at both the project level and the
   journal article level was not carried out in the majority of cases, and
   when sharing was accomplished, the shared data were often of
   questionable usability due to access, documentation, and formatting
   issues. We close the article by offering recommendations for how data
   producers, journal publishers, data repositories, and funding agencies
   can facilitate the process of sharing data in a meaningful way.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Van Tuyl, S (Corresponding Author), Oregon State Univ, Ctr Digital Scholarship \& Serv, Univ Lib, Corvallis, OR 97331 USA.
   Van Tuyl, Steven, Oregon State Univ, Ctr Digital Scholarship \& Serv, Univ Lib, Corvallis, OR 97331 USA.
   Whitmire, Amanda L., Stanford Univ, Hopkins Marine Stn, Harold A Miller Lib, Pacific Grove, CA 93950 USA.},
DOI = {10.1371/journal.pone.0147942},
Article-Number = {e0147942},
ISSN = {1932-6203},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {steve.vantuyl@oregonstate.edu},
Affiliations = {Oregon State University; Stanford University},
ResearcherID-Numbers = {Whitmire, Amanda L/H-7035-2012
   Van Tuyl, Steven/E-2814-2014},
ORCID-Numbers = {Whitmire, Amanda L/0000-0003-2429-8879
   Van Tuyl, Steven/0000-0002-8752-272X},
Funding-Acknowledgement = {Oregon State University Libraries \& Press Open Access Fund},
Funding-Text = {Publication of this article in an open access journal was funded by the
   Oregon State University Libraries \& Press Open Access Fund. The funders
   had no role in study design, data collection and analysis, decision to
   publish, or preparation of the manuscript.},
Number-of-Cited-References = {23},
Times-Cited = {27},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {24},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {DF3BJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000371218400011},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001071418400001,
Author = {Thompson, P. Travis and Moseley, Hunter N. B.},
Title = {MESSES: Software for Transforming Messy Research Datasets into Clean
   Submissions to Metabolomics Workbench for Public Sharing},
Journal = {METABOLITES},
Year = {2023},
Volume = {13},
Number = {7},
Month = {JUL},
Abstract = {In recent years, the FAIR guiding principles and the broader concept of
   open science has grown in importance in academic research, especially as
   funding entities have aggressively promoted public sharing of research
   products. Key to public research sharing is deposition of datasets into
   online data repositories, but it can be a chore to transform messy
   unstructured data into the forms required by these repositories. To help
   generate Metabolomics Workbench depositions, we have developed the
   MESSES (Metadata from Experimental SpreadSheets Extraction System)
   software package, implemented in the Python 3 programming language and
   supported on Linux, Windows, and Mac operating systems. MESSES helps
   transform tabular data from multiple sources into a Metabolomics
   Workbench specific deposition format. The package provides three
   commands, extract, validate, and convert, that implement a natural data
   transformation workflow. Moreover, MESSES facilitates richer metadata
   capture than is typically attempted by manual efforts. The source code
   and extensive documentation is hosted on GitHub and is also available on
   the Python Package Index for easy installation.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Moseley, HNB (Corresponding Author), Univ Kentucky, Superfund Res Ctr, Lexington, KY 40536 USA.
   Moseley, HNB (Corresponding Author), Univ Kentucky, Dept Mol \& Cellular Biochem, Lexington, KY 40536 USA.
   Moseley, HNB (Corresponding Author), Ctr Clin \& Translat Sci, Lexington, KY 40536 USA.
   Moseley, HNB (Corresponding Author), Univ Kentucky, Markey Canc Ctr, Lexington, KY 40536 USA.
   Moseley, HNB (Corresponding Author), Univ Kentucky, Inst Biomed Informat, Lexington, KY 40536 USA.
   Thompson, P. Travis; Moseley, Hunter N. B., Univ Kentucky, Superfund Res Ctr, Lexington, KY 40536 USA.
   Moseley, Hunter N. B., Univ Kentucky, Dept Mol \& Cellular Biochem, Lexington, KY 40536 USA.
   Moseley, Hunter N. B., Ctr Clin \& Translat Sci, Lexington, KY 40536 USA.
   Moseley, Hunter N. B., Univ Kentucky, Markey Canc Ctr, Lexington, KY 40536 USA.
   Moseley, Hunter N. B., Univ Kentucky, Inst Biomed Informat, Lexington, KY 40536 USA.},
DOI = {10.3390/metabo13070842},
Article-Number = {842},
EISSN = {2218-1989},
Keywords = {data sharing; dataset deposition; metadata capture; data transformation;
   Python programming language; Metabolomics Workbench},
Keywords-Plus = {METABOLIGHTS; REPOSITORY; STANDARDS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {hunter.moseley@uky.edu},
Affiliations = {University of Kentucky; University of Kentucky; University of Kentucky;
   University of Kentucky},
ORCID-Numbers = {Moseley, Hunter/0000-0003-3995-5368},
Funding-Acknowledgement = {The authors would like to acknowledge the large continual effort that
   Shankar Subramaniam, Eoin Fahy, and the whole MW/UC San Diego team have
   put into maintaining and expanding the repository.},
Funding-Text = {The authors would like to acknowledge the large continual effort that
   Shankar Subramaniam, Eoin Fahy, and the whole MW/UC San Diego team have
   put into maintaining and expanding the repository.},
Number-of-Cited-References = {22},
Times-Cited = {0},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Metabolites},
Doc-Delivery-Number = {S5FH3},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001071418400001},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000266214000038,
Author = {Bohland, Jason W. and Wu, Caizhi and Barbas, Helen and Bokil, Hemant and
   Bota, Mihail and Breiter, Hans C. and Cline, Hollis T. and Doyle, John
   C. and Freed, Peter J. and Greenspan, Ralph J. and Haber, Suzanne N. and
   Hawrylycz, Michael and Herrera, Daniel G. and Hilgetag, Claus C. and
   Huang, Z. Josh and Jones, Allan and Jones, Edward G. and Karten, Harvey
   J. and Kleinfeld, David and Kotter, Rolf and Lester, Henry A. and Lin,
   John M. and Mensh, Brett D. and Mikula, Shawn and Panksepp, Jaak and
   Price, Joseph L. and Safdieh, Joseph and Saper, Clifford B. and Schiff,
   Nicholas D. and Schmahmann, Jeremy D. and Stillman, Bruce W. and
   Svoboda, Karel and Swanson, Larry W. and Toga, Arthur W. and Van Essen,
   David C. and Watson, James D. and Mitra, Partha P.},
Title = {A Proposal for a Coordinated Effort for the Determination of Brainwide
   Neuroanatomical Connectivity in Model Organisms at a Mesoscopic Scale},
Journal = {PLOS COMPUTATIONAL BIOLOGY},
Year = {2009},
Volume = {5},
Number = {3},
Month = {MAR},
Abstract = {In this era of complete genomes, our knowledge of neuroanatomical
   circuitry remains surprisingly sparse. Such knowledge is critical,
   however, for both basic and clinical research into brain function. Here
   we advocate for a concerted effort to fill this gap, through systematic,
   experimental mapping of neural circuits at a mesoscopic scale of
   resolution suitable for comprehensive, brainwide coverage, using
   injections of tracers or viral vectors. We detail the scientific and
   medical rationale and briefly review existing knowledge and experimental
   techniques. We define a set of desiderata, including brainwide coverage;
   validated and extensible experimental techniques suitable for
   standardization and automation; centralized, open-access data
   repository; compatibility with existing resources; and tractability with
   current informatics technology. We discuss a hypothetical but tractable
   plan for mouse, additional efforts for the macaque, and technique
   development for human. We estimate that the mouse connectivity project
   could be completed within five years with a comparatively modest budget.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Review},
Language = {English},
Affiliation = {Bohland, JW (Corresponding Author), Cold Spring Harbor Lab, POB 100, Cold Spring Harbor, NY 11724 USA.
   Bohland, Jason W.; Wu, Caizhi; Bokil, Hemant; Cline, Hollis T.; Huang, Z. Josh; Lin, John M.; Stillman, Bruce W.; Watson, James D.; Mitra, Partha P., Cold Spring Harbor Lab, Cold Spring Harbor, NY 11724 USA.
   Barbas, Helen, Boston Univ, Dept Hlth Sci, Boston, MA 02215 USA.
   Bota, Mihail; Swanson, Larry W., Univ So Calif, Dept Biol Sci, Los Angeles, CA 90089 USA.
   Bokil, Hemant, Massachusetts Gen Hosp, Dept Radiol, Charlestown, MA USA.
   Doyle, John C., CALTECH, Dept Elect Engn, Pasadena, CA 91125 USA.
   Freed, Peter J., Columbia Univ, New York State Psychiat Inst, Med Ctr, New York, NY USA.
   Greenspan, Ralph J., Inst Neurosci, San Diego, CA USA.
   Haber, Suzanne N., Univ Rochester, Med Ctr, Dept Physiol \& Pharmacol, Rochester, NY 14642 USA.
   Hawrylycz, Michael; Jones, Allan, Allen Inst Brain Sci, Seattle, WA USA.
   Herrera, Daniel G., Harvard Univ, Brigham \& Womens Hosp, Dept Psychiat, Sch Med, Boston, MA 02115 USA.
   Hilgetag, Claus C., Jacobs Univ Bremen, Sch Sci \& Engn, Bremen, Germany.
   Jones, Edward G.; Mikula, Shawn, Univ Calif Davis, Ctr Neurosci, Davis, CA 95616 USA.
   Karten, Harvey J., Univ Calif San Diego, Sch Med, Dept Neurosci, La Jolla, CA 92093 USA.
   Kleinfeld, David, Univ Calif San Diego, Dept Phys, La Jolla, CA 92093 USA.
   Kotter, Rolf, Radboud Univ Nijmegen, Med Ctr, Donders Inst Brain Cognit \& Behav, Dept Cognit Neurosci,NeuroPI, NL-6525 ED Nijmegen, Netherlands.
   Lester, Henry A., CALTECH, Dept Biol, Pasadena, CA 91125 USA.
   Mensh, Brett D., Columbia Univ, Dept Psychiat, Med Ctr, New York, NY USA.
   Panksepp, Jaak, Washington State Univ, Coll Vet Med, Pullman, WA 99164 USA.
   Price, Joseph L.; Van Essen, David C., Washington Univ, Sch Med, Dept Anat \& Neurobiol, St Louis, MO 63110 USA.
   Safdieh, Joseph; Schiff, Nicholas D., Weill Cornell Med Coll, Dept Neurol, New York, NY USA.
   Saper, Clifford B., Beth Israel Deaconess Med Ctr, Dept Neurol, Boston, MA 02215 USA.
   Schmahmann, Jeremy D., Massachusetts Gen Hosp, Dept Neurol, Boston, MA 02114 USA.
   Svoboda, Karel, Howard Hughes Med Inst, Ashburn, VA USA.
   Toga, Arthur W., Univ Calif Los Angeles, Sch Med, Dept Neurol, Lab NeuroImaging, Los Angeles, CA 90024 USA.},
DOI = {10.1371/journal.pcbi.1000334},
Article-Number = {e1000334},
ISSN = {1553-734X},
EISSN = {1553-7358},
Keywords-Plus = {BIOTINYLATED DEXTRAN-AMINE; NERVOUS-SYSTEM; WHITE-MATTER;
   CORPUS-CALLOSUM; ORGANIZATION; ANTEROGRADE; NEUROINFORMATICS;
   IDENTIFICATION; NEUROSCIENCE; POPULATIONS},
Research-Areas = {Biochemistry \& Molecular Biology; Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Mathematical \& Computational Biology},
Author-Email = {bohland@cshl.edu},
Affiliations = {Cold Spring Harbor Laboratory; Boston University; University of Southern
   California; Harvard University; Massachusetts General Hospital;
   California Institute of Technology; New York State Psychiatry Institute;
   Columbia University; University of Rochester; Allen Institute for Brain
   Science; Harvard University; Brigham \& Women's Hospital; Harvard
   Medical School; Jacobs University; University of California System;
   University of California Davis; University of California System;
   University of California San Diego; University of California System;
   University of California San Diego; Radboud University Nijmegen;
   California Institute of Technology; Columbia University; Washington
   State University; Washington University (WUSTL); Cornell University;
   Weill Cornell Medicine; Harvard University; Beth Israel Deaconess
   Medical Center; Harvard University; Massachusetts General Hospital;
   Howard Hughes Medical Institute; University of California System;
   University of California Los Angeles; University of California Los
   Angeles Medical Center; David Geffen School of Medicine at UCLA},
ResearcherID-Numbers = {Bohland, Jason W/L-4807-2016
   Kötter, Rolf/A-2565-2010
   Barbas, Helen/JAX-4703-2023
   Greenspan, Ralph/JBI-9487-2023
   Van Essen, David/ABA-8888-2020
   Schmahmann, Jeremy/ABF-1215-2021
   Hilgetag, Claus C/AAH-1760-2020
   Doyle, John/IAQ-1764-2023
   Safdieh, Joseph/AAC-1854-2019
   Hilgetag, Claus C/L-7282-2013
   },
ORCID-Numbers = {Bohland, Jason W/0000-0002-6305-5848
   Schmahmann, Jeremy/0000-0003-0706-5125
   Hilgetag, Claus C/0000-0003-2129-8910
   Safdieh, Joseph/0000-0002-2495-2925
   Hilgetag, Claus C/0000-0003-2129-8910
   Barbas, Helen/0000-0003-0825-0832
   Huang, Z. Josh/0000-0003-0592-028X
   Stillman, Bruce/0000-0002-9453-4091
   Mitra, Partha/0000-0001-8818-6804
   karel, svoboda/0000-0002-6670-7362},
Funding-Acknowledgement = {W. M. Keck Foundation},
Funding-Text = {This paper is a result of discussions at the 2007 and 2008 Brain
   Architecture Project Banbury Center Meetings, funded by the W. M. Keck
   Foundation. The sponsors had no role in the conception or preparation of
   this manuscript.},
Number-of-Cited-References = {72},
Times-Cited = {202},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {36},
Journal-ISO = {PLoS Comput. Biol.},
Doc-Delivery-Number = {447TF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000266214000038},
OA = {Green Published, gold, Green Submitted, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:001054372100001,
Author = {Cannone, Carla and Allington, Lucy and Barron, Karla Cervantes and
   Charbonnier, Flora and Walker, Miriam Zachau and Halloran, Claire and
   Yeganyan, Rudolf and Tan, Naomi and Cullen, Jonathan M. and Harrison,
   John and To, Long Seng and Howells, Mark},
Title = {Designing a zero-order energy transition model: How to create a new
   Starter Data Kit},
Journal = {METHODSX},
Year = {2023},
Volume = {10},
Abstract = {The Paris Agreement was signed by 192 Parties, who committed to reducing
   emissions. Reaching such commitments by developing national
   decarbonisation strategies requires significant analyses and investment.
   Analyses for such strategies are often delayed due to a lack of accurate
   and upto-date data for creating energy transition models. The Starter
   Data Kits address this issue by providing open-source, zero-level
   country datasets to accelerate the energy planning process. There is a
   strong demand for replicating the process of creating Starter Data Kits
   because they are currently only available for 69 countries in Africa,
   Asia, and South America. Using an African country as an example, this
   paper presents the methodology to create a Starter Data Kit made of
   tool-agnostic data repositories and OSeMOSYS-specific data files. The
   paper illustrates the steps involved, provides additional information
   for conducting similar work in Asia and South America, and highlights
   the limitations of the current version of the Starter Data Kits. Future
   development is proposed to expand the datasets, including new and more
   accurate data and new energy sectors. Therefore, this document provides
   instructions on the steps and materials required to develop a Starter
   Data Kit.\& BULL; The methodology presented here is intended to
   encourage practitioners to apply it to new countries and expand the
   current Starter Data Kits library.\& BULL; It is a novel process that
   creates data pipelines that feed into a single Data Collection and
   Manipulation Tool (DaCoMaTool).\& BULL; It allows for tool-agnostic data
   creation in a consistent format ready for a modelling analysis using one
   of the available tools.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Cannone, C (Corresponding Author), Loughborough Univ, Ctr Sustainable Transitions Energy Environm \& Resi, Loughborough, England.
   Cannone, C (Corresponding Author), Imperial Coll London, Ctr Environm Policy, London, England.
   Cannone, Carla; Allington, Lucy; Yeganyan, Rudolf; Tan, Naomi; Harrison, John; To, Long Seng; Howells, Mark, Loughborough Univ, Ctr Sustainable Transitions Energy Environm \& Resi, Loughborough, England.
   Cannone, Carla; Yeganyan, Rudolf; Tan, Naomi; Howells, Mark, Imperial Coll London, Ctr Environm Policy, London, England.
   Barron, Karla Cervantes; Cullen, Jonathan M., Univ Cambridge, Dept Engn, Cambridge, England.
   Charbonnier, Flora; Walker, Miriam Zachau; Halloran, Claire, Univ Oxford, Dept Engn Sci, Oxford, England.},
DOI = {10.1016/j.mex.2023.102120},
EarlyAccessDate = {MAR 2023},
Article-Number = {102120},
EISSN = {2215-0161},
Keywords = {Energy system modelling; Data collection tool; OSeMOSYS; clicSAND;
   U4RIA; open-access model; open-source; Climate Compatible Growth; data
   pipeline; Data2Deal; workflow},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {C.Cannone@lboro.ac.uk},
Affiliations = {Loughborough University; Imperial College London; University of
   Cambridge; University of Oxford},
ORCID-Numbers = {Cannone, Carla/0000-0002-1214-8913},
Funding-Acknowledgement = {Climate Compatible Growth Programme (\#CCG) of the UK's Foreign,
   Commonwealth \& Development Office (FCDO);  {[}CCG]},
Funding-Text = {This paper has been written with the support of the Climate Compatible
   Growth Programme (\#CCG) of the UK's Foreign, Com-monwealth \&
   Development Office (FCDO) . The views expressed in this paper do not
   necessarily reflect the UK government's official policies.},
Number-of-Cited-References = {45},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {MethodsX},
Doc-Delivery-Number = {Q0GF7},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001054372100001},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000608437800145,
Author = {Li, Cuiping and Tian, Dongmei and Tang, Bixia and Liu, Xiaonan and Teng,
   Xufei and Zhao, Wenming and Zhang, Zhang and Song, Shuhui},
Title = {Genome Variation Map: a worldwide collection of genome variations across
   multiple species},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2021},
Volume = {49},
Number = {D1},
Pages = {D1186-D1191},
Month = {JAN 8},
Abstract = {The Genome Variation Map (GVM; http://bigd.big.ac.cn/gvm/) is a public
   data repository of genome variations. It aims to collect and integrate
   genome variations for a wide range of species, accepts submissions of
   different variation types from all over the world and provides free open
   access to all publicly available data in support of worldwide research
   activities. Compared with the previous version, particularly, a total of
   22 species, 115 projects, 55 935 samples, 463 429 609 variants, 66 220
   associations and 56 submissions (as of 7 September 2020) were newly
   added in the current version of GVM. In the current release, GVM houses
   a total of similar to 960 million variants from 41 species, including 13
   animals, 25 plants and 3 viruses. Moreover, it incorporates 64 819
   individual genotypes and 260 393 manually curated high-quality
   genotype-to-phenotype associations. Since its inception, GVM has
   archived genomic variation data of 43 754 samples submitted by worldwide
   users and served >1 million data download requests. Collectively, as a
   core resource in the NationalGenomics Data Center, GVM provides valuable
   genome variations for a diversity of species and thus plays an important
   role in both functional genomics studies and molecular breeding.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Zhang, Z; Song, SH (Corresponding Author), China Natl Ctr Bioinformat, Beijing 100101, Peoples R China.
   Zhang, Z; Song, SH (Corresponding Author), Chinese Acad Sci, Natl Genom Data Ctr, Beijing Inst Genom, Beijing 100101, Peoples R China.
   Zhang, Z; Song, SH (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Z; Song, SH (Corresponding Author), Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Li, Cuiping; Tian, Dongmei; Tang, Bixia; Liu, Xiaonan; Teng, Xufei; Zhao, Wenming; Zhang, Zhang; Song, Shuhui, China Natl Ctr Bioinformat, Beijing 100101, Peoples R China.
   Li, Cuiping; Tian, Dongmei; Tang, Bixia; Liu, Xiaonan; Teng, Xufei; Zhao, Wenming; Zhang, Zhang; Song, Shuhui, Chinese Acad Sci, Natl Genom Data Ctr, Beijing Inst Genom, Beijing 100101, Peoples R China.
   Liu, Xiaonan; Teng, Xufei; Zhao, Wenming; Zhang, Zhang; Song, Shuhui, Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Liu, Xiaonan; Teng, Xufei; Zhao, Wenming; Zhang, Zhang; Song, Shuhui, Univ Chinese Acad Sci, Beijing 100049, Peoples R China.},
DOI = {10.1093/nar/gkaa1005},
ISSN = {0305-1048},
EISSN = {1362-4962},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {zhangzhang@big.ac.cn
   songshh@big.ac.cn},
Affiliations = {Chinese Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese
   Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese Academy
   of Sciences; University of Chinese Academy of Sciences, CAS},
ResearcherID-Numbers = {Zhang, Zhang/JAX-2097-2023
   Teng, Xufei/JMQ-0733-2023
   tian, dongmei/HIR-8892-2022
   zhang, zheng/HCH-9684-2022
   song, shuhui/D-6015-2014
   zhang, zhang/GQZ-6804-2022
   },
ORCID-Numbers = {tian, dongmei/0000-0003-0564-625X
   Zhang, Zhang/0000-0001-6603-5060},
Funding-Acknowledgement = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDA24040201, XDA19090116, XDA19050302]; National Key R\&D Program of
   China {[}2020YFC0848900, 2018YFD1000505, 2017YFC0907502]; 13th Five-year
   Informatization Plan of Chinese Academy of Sciences {[}XXH13505-05];
   Genomics Data Center Construction of Chinese Academy of Sciences
   {[}XXH-13514-0202]; K.C. Wong Education Foundation; International
   Partnership Program of the Chinese Academy of Sciences
   {[}153F11KYSB20160008]; Youth Innovation Promotion Association of
   Chinese Academy of Science {[}2017141]; Strategic Priority Research
   Program of the Chinese Academy of Sciences},
Funding-Text = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDA24040201 to S.S., XDA19090116 to S.S., XDA19050302 to Z.Z.];
   National Key R\&D Program of China {[}2020YFC0848900, 2018YFD1000505,
   2017YFC0907502]; 13th Five-year Informatization Plan of Chinese Academy
   of Sciences {[}XXH13505-05]; Genomics Data Center Construction of
   Chinese Academy of Sciences {[}XXH-13514-0202]; K.C. Wong Education
   Foundation (to Z.Z.); International Partnership Program of the Chinese
   Academy of Sciences {[}153F11KYSB20160008]; Youth Innovation Promotion
   Association of Chinese Academy of Science {[}2017141 to S.S.]. Funding
   for open access charge: Strategic Priority Research Program of the
   Chinese Academy of Sciences.},
Number-of-Cited-References = {30},
Times-Cited = {28},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {16},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {PT2GR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000608437800145},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000684860900004,
Author = {Patonai, Katalin and Jordan, Ferenc},
Title = {Integrating trophic data from the literature: The Danube River food web},
Journal = {FOOD WEBS},
Year = {2021},
Volume = {28},
Month = {SEP},
Abstract = {In the era of bioinformatics and big data, ecological research depends
   on large and easily accessible databases that make it possible to
   construct complex system models. Open-access data repositories for food
   webs via publications and ecological databases (e.g. EcoBase) are
   becoming increasingly common, yet certain ecosystem types are
   underrepresented (e.g. rivers). In this paper, we compile the trophic
   connections (predator-prey relationships) for the Danube River ecosystem
   as gathered from globally available literature data. Data are analyzed
   by Danube regions separately (Upper, Middle, Lower Danube) as well as an
   integrated master network version. The master version has been
   aggregated into larger taxonomic categories. Local and global metrics
   were used to analyze and compare each network. We find disparity between
   regions (the Middle Danube having most nodes, but still quite
   heterogenous), we identify the most important trophic groups, and
   explain ways on evaluating missing data using each aggregation stage.
   This data-driven approach, summarizing our presently documented
   knowledge, can be used for preparing preliminary models and to further
   refine the Danube River food web in the future.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Jordán, F (Corresponding Author), Cent European Univ, Democracy Inst, Nador 13, H-1051 Budapest, Hungary.
   Patonai, Katalin, Eotvos Lorand Univ, Budapest, Hungary.
   Jordan, Ferenc, Cent European Univ, Democracy Inst, Nador 13, H-1051 Budapest, Hungary.
   Jordan, Ferenc, Stn Zool Anton Dohrn, Naples, Italy.},
DOI = {10.1016/j.fooweb.2021.e00203},
EarlyAccessDate = {JUL 2021},
Article-Number = {e00203},
ISSN = {2352-2496},
Keywords = {Aggregation; Danube River; Food web; Incomplete data; Taxonomy},
Keywords-Plus = {DYNAMICS},
Research-Areas = {Biodiversity \& Conservation; Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Biodiversity Conservation; Ecology},
Author-Email = {JordanF@ceu.edu},
Affiliations = {Eotvos Lorand University; Central European University; Stazione
   Zoologica Anton Dohrn di Napoli},
ResearcherID-Numbers = {Jordan, Ferenc/A-9940-2009
   },
ORCID-Numbers = {Jordan, Ferenc/0000-0002-0224-6472
   Patonai, Katalin/0000-0002-7248-7394},
Funding-Acknowledgement = {National Research, Development and Innovation Office (NKFIH)
   {[}GINOP-2.3.2-15-2016-00057]},
Funding-Text = {We acknowledge Anett Endredi for providing the R code template used for
   visualizing the food webs. Our research was supported by the National
   Research, Development and Innovation Office (NKFIH) grant
   GINOP-2.3.2-15-2016-00057.},
Number-of-Cited-References = {29},
Times-Cited = {4},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Food Webs},
Doc-Delivery-Number = {UA0MX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000684860900004},
DA = {2024-01-15},
}

@article{ WOS:000237658400010,
Author = {Coles, Simon J. and Frey, Jeremy G. and Hursthouse, Michel B. and Light,
   Mark E. and Milsted, Andrew J. and Carr, Leslie A. and DeRoure, David
   and Gutteridge, Christopher J. and Mills, Hugo R. and Meacham, Ken E.
   and Surridge, Michael and Lyon, Elizabeth and Heery, Rachel and Duke,
   Monica and Day, Michael},
Title = {An e-science environment for Service Crystallography - from submission
   to dissemination},
Journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING},
Year = {2006},
Volume = {46},
Number = {3},
Pages = {1006-1016},
Month = {MAY},
Abstract = {The U. K. National Crystallography Service (NCS) has developed a
   prototype e-science infrastructure for the provision of a small molecule
   crystallography service from sample receipt to results dissemination.
   This paper outlines the two strands of this service, which ( a) enable a
   user to contribute in the conduction of an experiment and (b) provide an
   effective route for the archival and dissemination of the arising
   results. Access to use the NCS facilities and expertise and a mechanism
   to submit samples is granted through a secure Grid infrastructure, which
   seamlessly provides instantaneous feedback and the ability to remotely
   monitor and guide diffraction experiments and stage the diffraction data
   to a securely accessible location. Publication of all the data and
   results generated during the course of the experiment, from processed
   data to analyzed structures, is then enabled by means of an open access
   data repository. The repository publishes its content through
   established digital libraries' protocols, which enable harvester and
   aggregator services to make the data searchable and accessible.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Coles, SJ (Corresponding Author), Univ Southampton, Sch Chem, Southampton SO17 1BJ, Hants, England.
   Univ Southampton, Sch Chem, Southampton SO17 1BJ, Hants, England.
   Univ Southampton, Sch Elect \& Comp Sci, Southampton SO17 1BJ, Hants, England.
   Univ Southampton, IT Innovat Ctr, Southampton SO16 7NP, Hants, England.
   Univ Bath, UKOLN, Bath BA2 7AY, Avon, England.},
DOI = {10.1021/ci050362w},
ISSN = {1549-9596},
EISSN = {1549-960X},
Keywords-Plus = {CRYSTAL-STRUCTURES; DATABASE; VALIDATION},
Research-Areas = {Pharmacology \& Pharmacy; Chemistry; Computer Science},
Web-of-Science-Categories  = {Chemistry, Medicinal; Chemistry, Multidisciplinary; Computer Science,
   Information Systems; Computer Science, Interdisciplinary Applications},
Author-Email = {s.j.coles@soton.ac.uk},
Affiliations = {University of Southampton; University of Southampton; University of
   Southampton; University of Bath},
ResearcherID-Numbers = {Day, Michael W/C-3029-2009
   Frey, Jeremy G./ABC-1436-2021
   Coles, Simon/A-1795-2009
   De Roure, David/D-6785-2011
   Frey, Jeremy G/B-8630-2011
   Hursthouse, Michael B/B-9885-2011
   Milsted, Andrew J/C-9686-2010
   Coles, Simon/AAI-7820-2020
   Light, Mark E/B-6555-2009
   },
ORCID-Numbers = {Day, Michael W/0000-0002-1443-5334
   Frey, Jeremy G./0000-0003-0842-4302
   Coles, Simon/0000-0001-8414-9272
   De Roure, David/0000-0001-9074-3016
   Frey, Jeremy G/0000-0003-0842-4302
   Hursthouse, Michael B/0000-0002-9492-054X
   Coles, Simon/0000-0001-8414-9272
   Light, Mark E/0000-0002-0585-0843
   Duke, Monica/0000-0003-2588-7544
   Carr, Leslie/0000-0002-2113-9680
   Milsted, Andrew/0000-0003-4693-8785},
Funding-Acknowledgement = {Engineering and Physical Sciences Research Council {[}EP/C007271/1]
   Funding Source: researchfish},
Number-of-Cited-References = {31},
Times-Cited = {28},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {J. Chem Inf. Model.},
Doc-Delivery-Number = {044FS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000237658400010},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000720624200033,
Author = {Pereira, Catarina and Mazein, Alexander and Farinha, Carlos M. and Gray,
   Michael A. and Kunzelmann, Karl and Ostaszewski, Marek and Balaur, Irina
   and Amaral, Margarida D. and Falcao, Andre O.},
Title = {CyFi-MAP: an interactive pathway-based resource for cystic fibrosis},
Journal = {SCIENTIFIC REPORTS},
Year = {2021},
Volume = {11},
Number = {1},
Month = {NOV 15},
Abstract = {Cystic fibrosis (CF) is a life-threatening autosomal recessive disease
   caused by more than 2100 mutations in the CF transmembrane conductance
   regulator (CFTR) gene, generating variability in disease severity among
   individuals with CF sharing the same CFTR genotype. Systems biology can
   assist in the collection and visualization of CF data to extract
   additional biological significance and find novel therapeutic targets.
   Here, we present the CyFi-MAP-a disease map repository of CFTR molecular
   mechanisms and pathways involved in CF. Specifically, we represented the
   wild-type (wt-CFTR) and the F508del associated processes (F508del-CFTR)
   in separate submaps, with pathways related to protein biosynthesis,
   endoplasmic reticulum retention, export, activation/inactivation of
   channel function, and recycling/degradation after endocytosis. CyFi-MAP
   is an open-access resource with specific, curated and continuously
   updated information on CFTR-related pathways available online at . This
   tool was developed as a reference CF pathway data repository to be
   continuously updated and used worldwide in CF research.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Falcao, AO (Corresponding Author), Univ Lisbon, Fac Sci, BioISI Biosyst Integrat Sci Inst, P-1749016 Lisbon, Portugal.
   Falcao, AO (Corresponding Author), Univ Lisbon, Fac Sci, LASIGE, P-1749016 Lisbon, Portugal.
   Pereira, Catarina; Farinha, Carlos M.; Amaral, Margarida D.; Falcao, Andre O., Univ Lisbon, Fac Sci, BioISI Biosyst Integrat Sci Inst, P-1749016 Lisbon, Portugal.
   Pereira, Catarina; Falcao, Andre O., Univ Lisbon, Fac Sci, LASIGE, P-1749016 Lisbon, Portugal.
   Mazein, Alexander; Ostaszewski, Marek; Balaur, Irina, Univ Luxembourg, Luxembourg Ctr Syst Biomed, 6 Ave Swing, L-4367 Belvaux, Luxembourg.
   Mazein, Alexander; Balaur, Irina, Univ Lyon, CIRI, UMR5308, CNRS ENS UCBL INSERM,European Inst Syst Biol \& Me, 50 Ave Tony Garnier, F-69007 Lyon, France.
   Gray, Michael A., Newcastle Univ, Biosci Inst, Univ Med Sch, Framlington Pl, Newcastle Upon Tyne NE2 4HH, Tyne \& Wear, England.
   Kunzelmann, Karl, Univ Regensburg, D-9147 Regensburg, Germany.},
DOI = {10.1038/s41598-021-01618-3},
Article-Number = {22223},
ISSN = {2045-2322},
Keywords-Plus = {TRANSMEMBRANE CONDUCTANCE REGULATOR; AIRWAY SURFACE LIQUID;
   PROTEIN-KINASE-C; QUALITY-CONTROL; CFTR; TRAFFICKING; ACTIVATION;
   BIOLOGY; PHOSPHORYLATION; WIKIPATHWAYS},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {aofalcao@ciencias.ulisboa.pt},
Affiliations = {BIOISI; Universidade de Lisboa; Universidade de Lisboa; University of
   Luxembourg; Centre National de la Recherche Scientifique (CNRS); CNRS -
   National Institute for Biology (INSB); Universite Claude Bernard Lyon 1;
   Institut National de la Sante et de la Recherche Medicale (Inserm);
   Ecole Normale Superieure de Lyon (ENS de LYON); Newcastle University -
   UK; University of Regensburg},
ResearcherID-Numbers = {Mazein, Alexander/C-1369-2013
   Farinha, Carlos/A-7110-2010
   Amaral, Margarida D/IZD-9935-2023
   Falcao, Andre/A-3545-2010
   Pereira, Catarina IV/K-2222-2016
   },
ORCID-Numbers = {Mazein, Alexander/0000-0001-7137-4171
   Farinha, Carlos/0000-0002-5467-1710
   Amaral, Margarida D/0000-0002-0828-8630
   Falcao, Andre/0000-0002-3588-8746
   Pereira, Catarina IV/0000-0002-8437-7432
   Balaur, Irina/0000-0002-3671-895X
   Ostaszewski, Marek/0000-0003-1473-370X},
Funding-Acknowledgement = {FCT/MCTES Portugal {[}UIDB/04046/2020, UIDP/04046/2020]; LASIGE Research
   Unit {[}UIDB/00408/2020, UIDP/00408/2020]; Innovative Medicines
   Initiative Joint Undertaking from the European Union {[}IMI 115446]; 
   {[}SFRH/PD/BD/131405/2017]},
Funding-Text = {The authors would like to thank the domain experts that participated in
   stimulating discussions and valuable feedback and to the colleagues from
   FunGP-Functional Genomics and Proteostasis who tested CyFi-MAP and
   provided valuable suggestions. Work in MDA lab is supported by
   UIDB/04046/2020 and UIDP/04046/2020 centre grants (to BioISI) from
   FCT/MCTES Portugal. CP was recipient of fellowship
   SFRH/PD/BD/131405/2017 and through funding of LASIGE Research Unit, ref.
   UIDB/00408/2020 and ref. UIDP/00408/2020. AM and IB were supported in
   part by the Innovative Medicines Initiative Joint Undertaking under
   Grant Agreement No. IMI 115446 (eTRIKS), resources of which are composed
   of financial contributions from the European Union's Seventh Framework
   Programme (FP7/2007-2013) and EFPIA companies.},
Number-of-Cited-References = {82},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Sci Rep},
Doc-Delivery-Number = {XA4MX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000720624200033},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:001003155800001,
Author = {Stallman, Jeffery K. K. and Robinson, Kyra},
Title = {Importance of Seasonal Variation in Hawaiian Mushroom (Agaricomycetes)
   Basidiomata Production for Biodiversity Discovery and Conservation},
Journal = {FRONTIERS IN FUNGAL BIOLOGY},
Year = {2022},
Volume = {3},
Month = {APR 4},
Abstract = {The Hawaiian Islands have a relatively well-known funga for a tropical
   location, yet there are over 400 species of mushrooms (Agaricomycetes)
   in the archipelago that remain to be documented. Importantly, the
   International Union for Conservation of Nature (IUCN) recently evaluated
   six mushrooms endemic to the islands as threatened with extinction. To
   improve detection of mushrooms for biodiversity discovery and better
   monitor threatened species in the archipelago-where many localities lack
   strong annual precipitation patterns associated with an obvious season
   for increased mushroom basidiomata production-we examined the phenology
   of Hawaiian mushrooms. Monthly richness was determined from a literature
   review and abundance from online data repositories. Phenological
   patterns were separately explored for native species and differing
   elevation and annual precipitation categories. Despite relatively
   consistent monthly temperatures and areas with regular monthly rainfall,
   we found Hawaiian mushrooms generally exhibit uneven temporal patterns
   in basidiomata production: richness and abundance are generally highest
   in January and lowest from February to April, then usually increase from
   May to July and remain at elevated levels through December. This pattern
   does not occur when considering native species richness only, nor when
   examining abundance data stratified by elevation and annual rainfall
   categories. Increased monthly basidiomata abundance in low elevation
   (<1,000 m), dry (<1,000 mm rainfall/year) locations on O'ahu and low,
   mesic (1,000-2,500 mm rainfall/year) locations on O'ahu and Kaua'i are
   positively correlated with increased monthly rainfall. Phenology of
   macrofungal sporocarp production should potentially be included in
   species threat assessments by the IUCN to increase detection via
   traditional surveying methods.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Stallman, JK (Corresponding Author), Purdue Univ, Dept Bot \& Plant Pathol, W Lafayette, IN 47907 USA.
   Stallman, Jeffery K. K., Purdue Univ, Dept Bot \& Plant Pathol, W Lafayette, IN 47907 USA.
   Robinson, Kyra, Univ Hawaii, Dept Biol, Hilo, HI USA.},
DOI = {10.3389/ffunb.2022.869689},
Article-Number = {869689},
EISSN = {2673-6128},
Keywords = {endangered species; fungi; Hawai'i; Hygrophoraceae; Pacific},
Research-Areas = {Mycology},
Web-of-Science-Categories  = {Mycology},
Author-Email = {jstallma@purdue.edu},
Affiliations = {Purdue University System; Purdue University West Lafayette Campus;
   Purdue University; University of Hawaii System; University Hawaii Hilo},
ORCID-Numbers = {Stallman, Jeffery/0000-0003-4713-2193},
Funding-Acknowledgement = {Purdue University Libraries Open Access Publishing Fund},
Funding-Text = {This article was funded in part by Purdue University Libraries Open
   Access Publishing Fund.},
Number-of-Cited-References = {39},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Front. Fungal Biol.},
Doc-Delivery-Number = {I5JZ7},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001003155800001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001053894700001,
Author = {Minchin, Jamie and Harris, Gavin H. and Baumann, Sasha and Smith, Emily
   R.},
Title = {Exclusion of pregnant people from emergency vaccine clinical trials: A
   systematic review of clinical trial protocols and reporting from 2009 to
   2019},
Journal = {VACCINE},
Year = {2023},
Volume = {41},
Number = {35},
Pages = {5159-5181},
Month = {AUG 7},
Abstract = {Background: Existing ethics guidance and regulatory requirements
   emphasize the need for pregnancyspecific safety and efficacy data during
   the development of vaccines in health emergencies. Our objective was to
   conduct a systematic review of vaccine clinical trials during active
   epidemic periods. Methods: We searched for Phase II and Phase III
   vaccine clinical trials initiated during the H1N1 influenza, Middle East
   Respiratory Syndrome Coronavirus (MERS-CoV), Zika, and Ebola virus
   disease (EVD) outbreaks from 2009 to 2019. Data were extracted from
   clinical trial protocols identified in the following registries:
   ClinicalTrials.gov, Pan African Clinical Trial Registry (PACTR), and all
   primary registries indicated by the World Health Organization's
   International Clinical Trials Registry Platform (ICTRP). Published
   studies from registered clinical trials were located through PubMed.
   Data was extracted on eligibility criteria and pregnancy outcomes. Data
   from this study is available in the Center for Open Science Data
   Repository:
   https://osf.io/nfk2p/?view\_only=47deb3b206724af9b46c9c0c0083a267.
   Results: We identified 96 vaccine clinical trial protocols and included
   84 in analysis. 5 records were excluded in screening for irrelevant
   abstracts, 7 were excluded in full-text assessment (1 for a therapeutic
   drug trial, 3 for enrolling elderly adults only, 3 for enrolling
   children/adolescents only). There were no eligible trials for MERS-CoV
   or Zika virus vaccines. Overall, 8 protocols explicitly included
   pregnant people; of these, 3 were completed trials with published
   results. Incidental pregnancies and outcomes of pregnant participants
   were reported in 2 studies, 10 studies reported serious adverse events
   related to pregnancy without mentioning total incidental pregnancies. A
   total of 411 recorded pregnancy outcomes were reported, with 293 from
   the 3 pregnancy-eligible studies with results. 71 serious adverse events
   pertaining to pregnancy were reported from all clinical trials with
   results. Conclusion: Pregnant people are underrepresented in vaccine
   clinical trials conducted during outbreaks, resulting in underreporting
   of pregnancy-related outcomes and a lack of protection for pregnant
   people and neonates from infectious diseases. \& COPY; 2023 The Authors.
   Published by Elsevier Ltd. This is an open access article under the CC
   BY license (http:// creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Smith, ER (Corresponding Author), George Washington Univ, Milken Inst, Sch Publ Hlth, 950 New Hampshire Ave NW, Washington, DC 20051 USA.
   Minchin, Jamie; Baumann, Sasha; Smith, Emily R., George Washington Univ, Milken Inst, Sch Publ Hlth, Dept Global Hlth, Washington, DC USA.
   Harris, Gavin H., Emory Univ, Sch Med, Dept Med, Atlanta, GA USA.
   Smith, Emily R., George Washington Univ, Milken Inst, Sch Publ Hlth, 950 New Hampshire Ave NW, Washington, DC 20051 USA.},
DOI = {10.1016/j.vaccine.2023.06.073},
EarlyAccessDate = {AUG 2023},
ISSN = {0264-410X},
EISSN = {1873-2518},
Keywords = {Ebola; Epidemics; Pregnancy; Vaccines; Zika},
Keywords-Plus = {RESPIRATORY SYNDROME CORONAVIRUS; IMMUNE-RESPONSE; H1N1 INFLUENZA;
   WOMEN; SAFETY; VIRUS; INFECTION; IMMUNOGENICITY; IMMUNIZATION;
   COLLECTION},
Research-Areas = {Immunology; Research \& Experimental Medicine},
Web-of-Science-Categories  = {Immunology; Medicine, Research \& Experimental},
Author-Email = {emilysmith@gwu.edu},
Affiliations = {George Washington University; Emory University; George Washington
   University},
ORCID-Numbers = {Smith, Emily/0000-0001-5715-9459
   Minchin, Jamie/0000-0002-2122-0366},
Number-of-Cited-References = {70},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Vaccine},
Doc-Delivery-Number = {P9OH7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001053894700001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000938273100009,
Author = {Tsueng, Ginger and Cano, Marco A. Alvarado and Bento, Jose and Czech,
   Candice and Kang, Mengjia and Pache, Lars and Rasmussen, V, Luke and
   Savidge, Tor C. and Starren, Justin and Wu, Qinglong and Xin, Jiwen R.
   and Yeaman, Michael and Zhou, Xinghua I. and Su, I, Andrew and Wu,
   Chunlei and Brown, Liliana and Shabman, Reed S. and Hughes, Laura D. and
   NIAID Syst Biol Data Disseminat},
Title = {Developing a standardized but extendable framework to increase the
   findability of infectious disease datasets},
Journal = {SCIENTIFIC DATA},
Year = {2023},
Volume = {10},
Number = {1},
Month = {FEB 23},
Abstract = {Biomedical datasets are increasing in size, stored in many repositories,
   and face challenges in FAIRness (findability, accessibility,
   interoperability, reusability). As a Consortium of infectious disease
   researchers from 15 Centers, we aim to adopt open science practices to
   promote transparency, encourage reproducibility, and accelerate research
   advances through data reuse. To improve FAIRness of our datasets and
   computational tools, we evaluated metadata standards across established
   biomedical data repositories. The vast majority do not adhere to a
   single standard, such as Schema.org, which is widely-adopted by
   generalist repositories. Consequently, datasets in these repositories
   are not findable in aggregation projects like Google Dataset Search. We
   alleviated this gap by creating a reusable metadata schema based on
   Schema.org and catalogued nearly 400 datasets and computational tools we
   collected. The approach is easily reusable to create schemas
   interoperable with community standards, but customized to a particular
   context. Our approach enabled data discovery, increased the reusability
   of datasets from a large research consortium, and accelerated research.
   Lastly, we discuss ongoing challenges with FAIRness beyond
   discoverability.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Tsueng, G; Hughes, LD (Corresponding Author), Scripps Res Inst, Dept Integrat Struct \& Computat Biol, La Jolla, CA 92037 USA.
   Tsueng, Ginger; Cano, Marco A. Alvarado; Czech, Candice; Xin, Jiwen R.; Zhou, Xinghua I.; Su, Andrew, I; Wu, Chunlei; Hughes, Laura D., Scripps Res Inst, Dept Integrat Struct \& Computat Biol, La Jolla, CA 92037 USA.
   Bento, Jose, Boston Coll, Dept Comp Sci, 245 Beacon St, Chestnut Hill, MA 02467 USA.
   Kang, Mengjia, Northwestern Univ, Feinberg Sch Med, Div Pulm \& Crit Care, Chicago, IL 60611 USA.
   Pache, Lars, Sanford Burnham Prebys Med Discovery Inst, Infect \& Inflammatory Dis Ctr, Immun \& Pathogenesis Program, La Jolla, CA 92037 USA.
   Rasmussen, Luke, V; Starren, Justin, Northwestern Univ, Dept Prevent Med, Feinberg Sch Med, Chicago, IL 60611 USA.
   Savidge, Tor C.; Wu, Qinglong, Baylor Coll Med, Texas Childrens Microbiome Ctr, Houston, TX 77030 USA.
   Savidge, Tor C.; Wu, Qinglong, Baylor Coll Med, Dept Pathol \& Immunol, Houston, TX 77030 USA.
   Yeaman, Michael, Univ Calif Los Angeles, David Geffen Sch Med, Dept Med, Los Angeles, CA 90095 USA.
   Yeaman, Michael, Harbor UCLA, Div Mol Med \& Infect Dis, Med Ctr, Torrance, CA 90502 USA.
   Yeaman, Michael, UCLA, Lundquist Inst Infect \& Immun Harbor, Med Ctr, Torrance, CA 90502 USA.
   Su, Andrew, I; Wu, Chunlei, Scripps Res Translat Inst, La Jolla, CA 92037 USA.
   Su, Andrew, I; Wu, Chunlei, Scripps Res Inst, Dept Mol Med, La Jolla, CA 92037 USA.
   Brown, Liliana; Shabman, Reed S., Natl Inst Allergy \& Infect Dis, Off Genom \& Adv Technol, Rockville, MD 20852 USA.},
DOI = {10.1038/s41597-023-01968-9},
Article-Number = {99},
EISSN = {2052-4463},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {gtsueng@scripps.edu
   lhughes@scripps.edu},
Affiliations = {Scripps Research Institute; Boston College; Northwestern University;
   Feinberg School of Medicine; Sanford Burnham Prebys Medical Discovery
   Institute; Northwestern University; Feinberg School of Medicine; Baylor
   College of Medicine; Baylor College of Medicine; University of
   California System; University of California Los Angeles; University of
   California Los Angeles Medical Center; David Geffen School of Medicine
   at UCLA; University of California System; University of California Los
   Angeles; University of California Los Angeles Medical Center; University
   of California System; University of California Los Angeles; Scripps
   Research Institute; National Institutes of Health (NIH) - USA; NIH
   National Institute of Allergy \& Infectious Diseases (NIAID)},
ORCID-Numbers = {Rasmussen, Luke/0000-0002-4497-8049
   Kang, Mengjia/0000-0002-1679-9473},
Funding-Acknowledgement = {National Institute of Allergy and Infectious Diseases (NIAID); National
   Institutes of Health (NIH) {[}U01 AI124290, U01 AI124302, U19 AI135995,
   U19 AI135964, U19 AI135972, U01 AI124319, 75N91019D00024]; National
   Center for Advancing Translational Sciences NIH {[}U24 TR002306];
   National Institute of General Medical Sciences {[}R01 GM083924]},
Funding-Text = {This work was supported in part by the National Institute of Allergy and
   Infectious Diseases (NIAID), National Institutes of Health (NIH) grants
   U01 AI124290 (Baylor: TS, QW), U01 AI124302 (Boston College: JB), U19
   AI135995 (Scripps Research: MAAC, LDH, GT, AIS, CW, JX, XZ), U19
   AI135964 (Northwestern: MK, LVR, JS), U19 AI135972 (Sanford Burnham
   Prebys: LP); U01 AI124319 (UCLA: MY), 75N91019D00024 (Scripps Research:
   CZ, GT, LDH, AIS, CW); National Center for Advancing Translational
   Sciences NIH grant U24 TR002306 (Scripps Research: MAAC, LDH, GT, AIS,
   CW, JX, XZ); and National Institute of General Medical Sciences grant
   R01 GM083924 (Scripps Research: MAAC, GT, AIS, CW, JX, XZ). We
   acknowledge the NIAID/DMID Systems Biology Consortium for Infectious
   Diseases Data Dissemination Working Group for developing the NIAID
   SysBio schemas, registering center-created datasets and computational
   tools, and providing critical feedback on the manuscript. We thank Reed
   Shabman for his leadership within the Data Dissemination Working Group,
   coordinating with centers to register datasets and tools, and helpful
   comments and careful revisions of the paper. We additionally thank
   Liliana Brown for the support of the Program this paper originated from
   and Serdar Turkarslan, Ishwar Chandramouliswaran, Wilbert van Panhuis,
   and Jack DiGiovanna for helpful discussions in preparing this
   manuscript.},
Number-of-Cited-References = {89},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Sci. Data},
Doc-Delivery-Number = {9G6PT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000938273100009},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:001004963500001,
Author = {Jeddi, Maryam Zare and Galea, Karen S. and Viegas, Susana and Fantke,
   Peter and Louro, Henriqueta and Theunis, Jan and Govarts, Eva and Denys,
   Sebastien and Fillol, Clemence and Rambaud, Loic and Kolossa-Gehring,
   Marike and Santonen, Tiina and van der Voet, Hilko and Ghosh, Manosij
   and Costa, Carla and Teixeira, Joao Paulo and Verhagen, Hans and Duca,
   Radu-Corneliu and Van Nieuwenhuyse, An and Jones, Kate and Sams, Craig
   and Sepai, Ovnair and Tranfo, Giovanna and Bakker, Martine and Palmen,
   Nicole and van Klaveren, Jacob and Scheepers, Paul T. J. and Paini,
   Alicia and Canova, Cristina and von Goetz, Natalie and Katsonouri,
   Andromachi and Karakitsios, Spyros and Sarigiannis, Dimosthenis A. and
   Bessems, Jos and Machera, Kyriaki and Harrad, Stuart and Hopf, Nancy B.},
Title = {FAIR environmental and health registry (FAIREHR)- supporting the science
   to policy interface and life science research, development and
   innovation},
Journal = {FRONTIERS IN TOXICOLOGY},
Year = {2023},
Volume = {5},
Month = {JUN 5},
Abstract = {The environmental impact on health is an inevitable by-product of human
   activity. Environmental health sciences is a multidisciplinary field
   addressing complex issues on how people are exposed to hazardous
   chemicals that can potentially affect adversely the health of present
   and future generations. Exposure sciences and environmental epidemiology
   are becoming increasingly data-driven and their efficiency and
   effectiveness can significantly improve by implementing the FAIR
   (findable, accessible, interoperable, reusable) principles for
   scientific data management and stewardship. This will enable data
   integration, interoperability and (re)use while also facilitating the
   use of new and powerful analytical tools such as artificial intelligence
   and machine learning in the benefit of public health policy, and
   research, development and innovation (RDI). Early research planning is
   critical to ensuring data is FAIR at the outset. This entails a
   well-informed and planned strategy concerning the identification of
   appropriate data and metadata to be gathered, along with established
   procedures for their collection, documentation, and management.
   Furthermore, suitable approaches must be implemented to evaluate and
   ensure the quality of the data. Therefore, the `Europe Regional Chapter
   of the International Society of Exposure Science' (ISES Europe) human
   biomonitoring working group (ISES Europe HBM WG) proposes the
   development of a FAIR Environment and health registry (FAIREHR)
   (hereafter FAIREHR). FAIR Environment and health registry offers
   preregistration of studies on exposure sciences and environmental
   epidemiology using HBM (as a starting point) across all areas of
   environmental and occupational health globally. The registry is proposed
   to receive a dedicated web-based interface, to be electronically
   searchable and to be available to all relevant data providers, users and
   stakeholders. Planned Human biomonitoring studies would ideally be
   registered before formal recruitment of study participants. The
   resulting FAIREHR would contain public records of metadata such as study
   design, data management, an audit trail of major changes to planned
   methods, details of when the study will be completed, and links to
   resulting publications and data repositories when provided by the
   authors. The FAIREHR would function as an integrated platform designed
   to cater to the needs of scientists, companies, publishers, and
   policymakers by providing user-friendly features. The implementation of
   FAIREHR is expected to yield significant benefits in terms of enabling
   more effective utilization of human biomonitoring (HBM) data.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Jeddi, MZ (Corresponding Author), Natl Inst Publ Hlth \& Environm RIVM, Bilthoven, Netherlands.
   Jeddi, Maryam Zare; Bakker, Martine; Palmen, Nicole; van Klaveren, Jacob, Natl Inst Publ Hlth \& Environm RIVM, Bilthoven, Netherlands.
   Galea, Karen S., Inst Occupat Med IOM, Res Ave North, Riccarton, Scotland.
   Viegas, Susana, NOVA Univ Lisbon, Comprehens Hlth Res Ctr, Publ Hlth Res Ctr, NOVA Natl Sch Publ Hlth,CHRC, Lisbon, Portugal.
   Fantke, Peter, Tech Univ Denmark, Dept Environm \& Resource Engn, Quantitat Sustainabil Assessment, Lyngby, Denmark.
   Louro, Henriqueta, Natl Inst Hlth Dr Ricardo Jorge, Dept Human Genet, Lisbon, Portugal.
   Louro, Henriqueta, Univ NOVA Lisboa, Tox Ctr Toxicogen \& Human Hlth, NOVA Med Sch, Lisbon, Portugal.
   Theunis, Jan; Govarts, Eva; Bessems, Jos, Flemish Inst Technol Res VITO, VITO Hlth, Mol, Belgium.
   Denys, Sebastien; Fillol, Clemence; Rambaud, Loic, SpF Sante Publ France, Environm \& Occupat Hlth Div, St Maurice, France.
   Kolossa-Gehring, Marike, German Environm Agcy UBA, Dessau Rosslau, Germany.
   Santonen, Tiina, Finnish Inst Occupat Hlth FIOH, Helsinki, Finland.
   van der Voet, Hilko, Wageningen Univ \& Res, Biometris, Wageningen, Netherlands.
   Katholieke Univ Leuven, Dept Publ Hlth \& Primary Care, Environm \& Hlth, Leuven, Belgium.
   Natl Inst Hlth Dr Ricardo Jorge, Dept Environm Hlth, Porto, Portugal.
   Costa, Carla; Teixeira, Joao Paulo, Univ Porto, EPIUnit, Inst Saude Publ, Porto, Portugal.
   Univ Ulster, Nutr Innovat Ctr Food \& Hlth NICHE, Coleraine, North Ireland.
   Tech Univ Denmark, Natl Food Inst, Lyngby, Denmark.
   Food Safety \& Nutr Consultancy, Zeist, Netherlands.
   Lab Natl Sante LNS, Dept Hlth Protect, Dudelange, Luxembourg.
   HSE Hlth \& Safety Execut, Buxton, England.
   UK Hlth Secur Agcy, Radiat Chem \& Environm Hazards Div, Chilton, England.
   Italian Inst Accid Work INAIL, Dept Occupat \& Environm Med, Epidemiol \& Hyg, Monte PorzioCatone, RM, Italy.
   Radboud Univ Nijmegen, Radboud Inst Biol \& Environm Sci, Nijmegen, Netherlands.
   EsqLABS GmbH, Saterland, Germany.
   Univ Padua, Dept Cardiothoraco Vasc Sci \& Publ Hlth, Unit Biostat Epidemiol \& Publ Hlth, Padua, Italy.
   Fed Off Publ Hlth, Bern, Switzerland.
   Swiss Fed Inst Technol, Zurich, Switzerland.
   Minist Hlth, State Gen Lab, Nicosia, Cyprus.
   Aristotle Univ Thessaloniki, HERACLES Res Ctr Exposome \& Hlth, Ctr Interdisciplinary Res \& Innovat, Thessaloniki, Greece.
   Univ Sch Adv Studies IUSS, Complex Risk \& Data Anal Res Ctr, Pavia, Italy.
   Benaki Phytopathol Inst, Dept Pesticides Control \& Phytopharmacy, Lab Pesticides Toxicol, Kifisia, Greece.
   Univ Birmingham, Sch Geog Earth \& Environm Sci, Birmingham, England.
   Univ Lausanne, Ctr Primary Care \& Publ Hlth Unisante, Lausanne, Switzerland.},
DOI = {10.3389/ftox.2023.1116707},
Article-Number = {1116707},
EISSN = {2673-3080},
Keywords = {open science; preregistration; environmental medicine; metadata;
   exposure science; data-driven decision making; exposure-disease
   continuum; real-world data},
Keywords-Plus = {RISK CHARACTERIZATION; EXPOSURE ASSESSMENT; BISPHENOL-A; INCIDENTS;
   WORKFLOW},
Research-Areas = {Toxicology},
Web-of-Science-Categories  = {Toxicology},
Author-Email = {maryam.zare.jeddi@rivm.nl},
Affiliations = {Netherlands National Institute for Public Health \& the Environment;
   Universidade Nova de Lisboa; Technical University of Denmark; Instituto
   Nacional de Saude Dr. Ricardo Jorge; Universidade Nova de Lisboa; VITO;
   Finnish Institute of Occupational Health; Wageningen University \&
   Research; KU Leuven; Instituto Nacional de Saude Dr. Ricardo Jorge;
   Universidade do Porto; Ulster University; Technical University of
   Denmark; UK Health Security Agency (UKHSA); Radboud University Nijmegen;
   University of Padua; Swiss Federal Institutes of Technology Domain; ETH
   Zurich; Aristotle University of Thessaloniki; IUSS PAVIA; University of
   Birmingham; University of Lausanne},
ResearcherID-Numbers = {van der Voet, Hilko/A-4073-2013
   Teixeira, Joao Paulo/F-5445-2013
   Costa, Carla/K-4048-2014
   Paini, Alicia/HDO-4070-2022
   Ghosh, Manosij/G-3374-2013
   Duca, Radu - Corneliu/F-3545-2017
   },
ORCID-Numbers = {van der Voet, Hilko/0000-0003-0802-7382
   Teixeira, Joao Paulo/0000-0001-8693-5250
   Costa, Carla/0000-0002-0027-8462
   Ghosh, Manosij/0000-0001-5034-001X
   Duca, Radu - Corneliu/0000-0002-9350-3816
   Harrad, Stuart/0000-0003-4650-0564
   Theunis, Jan/0000-0002-4191-5667},
Funding-Acknowledgement = {Safe and Efficient Chemistry by Design (SafeChem) - Swedish Foundation
   for Strategic Environmental Research {[}DIA 2018/11]; PARC project -
   under the European Union's Horizon Europe Research and Innovation
   program {[}101057014]},
Funding-Text = {Most co-authors were financialy supported with their respective
   inistitution. Some of the co-authors were financialy supportrd by the
   ``Safe and Efficient Chemistry by Design (SafeChem){''} project (grant
   no. DIA 2018/11) funded by the Swedish Foundation for Strategic
   Environmental Research, and by the PARC project (grant no. 101057014)
   funded under the European Union's Horizon Europe Research and Innovation
   program.},
Number-of-Cited-References = {51},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Front. Toxicol.},
Doc-Delivery-Number = {I8AR7},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001004963500001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000690270400001,
Author = {Schackart, III, Kenneth E. and Yoon, Jeong-Yeol},
Title = {Machine Learning Enhances the Performance of Bioreceptor-Free Biosensors},
Journal = {SENSORS},
Year = {2021},
Volume = {21},
Number = {16},
Month = {AUG},
Abstract = {Since their inception, biosensors have frequently employed simple
   regression models to calculate analyte composition based on the
   biosensor's signal magnitude. Traditionally, bioreceptors provide
   excellent sensitivity and specificity to the biosensor. Increasingly,
   however, bioreceptor-free biosensors have been developed for a wide
   range of applications. Without a bioreceptor, maintaining strong
   specificity and a low limit of detection have become the major
   challenge. Machine learning (ML) has been introduced to improve the
   performance of these biosensors, effectively replacing the bioreceptor
   with modeling to gain specificity. Here, we present how ML has been used
   to enhance the performance of these bioreceptor-free biosensors.
   Particularly, we discuss how ML has been used for imaging, Enose and
   Etongue, and surface-enhanced Raman spectroscopy (SERS) biosensors.
   Notably, principal component analysis (PCA) combined with support vector
   machine (SVM) and various artificial neural network (ANN) algorithms
   have shown outstanding performance in a variety of tasks. We anticipate
   that ML will continue to improve the performance of bioreceptor-free
   biosensors, especially with the prospects of sharing trained models and
   cloud computing for mobile computation. To facilitate this, the
   biosensing community would benefit from increased contributions to
   open-access data repositories for biosensor data.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Yoon, JY (Corresponding Author), Univ Arizona, Dept Biosyst Engn, Tucson, AZ 85721 USA.
   Yoon, JY (Corresponding Author), Univ Arizona, Dept Biomed Engn, Tucson, AZ 85721 USA.
   Schackart, Kenneth E., III; Yoon, Jeong-Yeol, Univ Arizona, Dept Biosyst Engn, Tucson, AZ 85721 USA.
   Yoon, Jeong-Yeol, Univ Arizona, Dept Biomed Engn, Tucson, AZ 85721 USA.},
DOI = {10.3390/s21165519},
Article-Number = {5519},
EISSN = {1424-8220},
Keywords = {label-free biosensor; machine learning; support vector machine;
   artificial neural network; principal component analysis},
Keywords-Plus = {ELECTRICAL-IMPEDANCE SPECTROSCOPY; ELECTRONIC NOSE; NEURAL-NETWORKS;
   LOC-SERS; E-TONGUE; ELECTROCHEMICAL BIOSENSORS; BIOELECTRONIC TONGUE;
   DRIFT COMPENSATION; QUANTITATIVE SERS; BREAST-TISSUE},
Research-Areas = {Chemistry; Engineering; Instruments \& Instrumentation},
Web-of-Science-Categories  = {Chemistry, Analytical; Engineering, Electrical \& Electronic;
   Instruments \& Instrumentation},
Author-Email = {schackartk@email.arizona.edu
   jyyoon@arizona.edu},
Affiliations = {University of Arizona; University of Arizona},
ORCID-Numbers = {Schackart, Kenneth/0000-0002-1658-3699},
Funding-Acknowledgement = {U.S. National Institutes ofHealth {[}T32GM132008]},
Funding-Text = {Thisworkwas supported by theU.S. National Institutes ofHealth under the
   grant T32GM132008.},
Number-of-Cited-References = {173},
Times-Cited = {29},
Usage-Count-Last-180-days = {9},
Usage-Count-Since-2013 = {89},
Journal-ISO = {Sensors},
Doc-Delivery-Number = {UH9WE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000690270400001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000363968000010,
Author = {Neville, Jon and Kopko, Steve and Broadbent, Steve and Aviles, Enrique
   and Stafford, Robert and Solinsky, Christine M. and Bain, Lisa J. and
   Cisneroz, Martin and Romero, Klaus and Stephenson, Diane and Coalition
   Major Dis},
Title = {Development of a unified clinical trial database for Alzheimer's disease},
Journal = {ALZHEIMERS \& DEMENTIA},
Year = {2015},
Volume = {11},
Number = {10},
Pages = {1212-1221},
Month = {OCT},
Abstract = {Introduction: Data obtained in completed Alzheimer's disease (AD)
   clinical trials can inform decision making for future trials.
   Recognizing the importance of sharing these data, the Coalition Against
   Major Diseases created an Online Data Repository for AD (CODR-AD) with
   the aim of supporting accelerated drug development. The aim of this
   study was to build an open access, standardized database from control
   arm data collected across many clinical trials.
   Methods: Comprehensive AD-specific data standards were developed to
   enable the pooling of data from different sources. Nine member
   organizations contributed patient-level data from 24 clinical trials of
   AD treatments.
   Results: CODR-AD consists of control arm pooled and standardized data
   from 24 trials currently numbered at 6500 subjects; Alzheimer's Disease
   Assessment Scale-cognitive subscale 11 is the main outcome and specific
   covariates are also included.
   Discussion: CODR-AD represents a unique integrated standardized clinical
   trials database available to qualified researchers. The pooling of data
   across studies facilitates a more comprehensive understanding of disease
   heterogeneity. (C) 2015 The Alzheimer's Association. Published by
   Elsevier Inc. All rights reserved.},
Publisher = {ELSEVIER SCIENCE INC},
Address = {STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA},
Type = {Article},
Language = {English},
Affiliation = {Stephenson, D (Corresponding Author), Crit Path Inst, Coalit Major Dis CAMD, Tucson, AZ 85718 USA.
   Neville, Jon; Broadbent, Steve; Aviles, Enrique; Stafford, Robert; Cisneroz, Martin; Romero, Klaus; Stephenson, Diane, Crit Path Inst, Coalit Major Dis CAMD, Tucson, AZ 85718 USA.
   Kopko, Steve, CDISC, Austin, TX USA.
   Solinsky, Christine M., USC Dept Pharmaceut Sci, Los Angeles, CA USA.},
DOI = {10.1016/j.jalz.2014.11.005},
ISSN = {1552-5260},
EISSN = {1552-5279},
Keywords = {Alzheimer's disease; Clinical trials database; Placebo data; Data
   standardization; Data integration; Facilitated access},
Keywords-Plus = {PATIENT-LEVEL; ADAS-COG; DRUG},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Clinical Neurology},
Author-Email = {Dstephenson@c-path.org},
Funding-Acknowledgement = {Science Foundation Arizona {[}SRG 0335-08]; U.S. Food and Drug
   Administration {[}5U01 FD003865]},
Funding-Text = {Partial funding for this work came from grants from Science Foundation
   Arizona (SRG 0335-08) and the U.S. Food and Drug Administration (5U01
   FD003865).},
Number-of-Cited-References = {31},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Alzheimers. Dement.},
Doc-Delivery-Number = {CV0UD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000363968000010},
DA = {2024-01-15},
}

@article{ WOS:000262371400004,
Author = {Yelitza Contreras, Hilda and Mendez, Zulay and Torrens, Rodrigo and
   Nunez, Luis A.},
Title = {BIOCLIMATIC NETWORK OF MERIDA STATE, VENEZUELA: ENVIRONMENTAL DATA
   RETRIEVAL, HANDLING AND PRESERVATION STRATEGIES},
Journal = {INTERCIENCIA},
Year = {2008},
Volume = {33},
Number = {11},
Pages = {795-801},
Month = {NOV},
Abstract = {This paper presents the experience accumulated in the construction and
   development of the Bioclimatic Network of the Merida State (Venezuela)
   as a test of concepts in the use of techniques and strategies for the
   retrieval, handling and preservation data from e-research. The ethical,
   conceptual and technical aspects involved in the preservation of the
   data are described, with emphasis on the concepts of open data and
   metadata, and, their standards. The construction of the bioclimatic data
   repository at www.cecals.ula.ve/redbc/ is reviewed, as well as its
   associated information products and some preliminary results and impacts
   of its utilization. Finally, some reflections and recommendations are
   made that will, perhaps, allow the maintenance and replication of this
   initiative.},
Publisher = {INTERCIENCIA},
Address = {APARTADO 51842, CARACAS 1050A, VENEZUELA},
Type = {Article},
Language = {Spanish},
Affiliation = {Núñez, LA (Corresponding Author), Corp Parque Tecnol Merida, Merida 5101, Venezuela.
   Nunez, Luis A., Univ Simon Bolivar, Caracas 1080, Venezuela.
   Yelitza Contreras, Hilda; Nunez, Luis A., UCV, Caracas, Venezuela.
   Nunez, Luis A., ULA, Fac Ciencias, Merida, Venezuela.
   Nunez, Luis A., ULA, Ctr Nacl Calculo Cient CECALCULA CPTM, Merida, Venezuela.
   Yelitza Contreras, Hilda, ULA, Fac Ingn, Merida, Venezuela.
   Yelitza Contreras, Hilda, ULA, CESIMO, Merida, Venezuela.
   Torrens, Rodrigo, CPTM, ULA, Ctr Teleinformac, Proyectos TIC, Merida, Venezuela.},
ISSN = {0378-1844},
Keywords-Plus = {E-SCIENCE},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {nunez@ula.ve},
Affiliations = {Simon Bolivar University; University of Central Venezuela; University of
   Los Andes Venezuela; University of Los Andes Venezuela; University of
   Los Andes Venezuela; University of Los Andes Venezuela; University of
   Los Andes Venezuela},
ResearcherID-Numbers = {Nunez, Luis A/D-3404-2013
   },
ORCID-Numbers = {Nunez, Luis A/0000-0003-4575-5899
   Torrens Heeren, Rodrigo/0000-0002-9351-7759},
Number-of-Cited-References = {33},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Interciencia},
Doc-Delivery-Number = {393KE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000262371400004},
DA = {2024-01-15},
}

@article{ WOS:000520137900006,
Author = {Damas, M. C. and Ngwira, C. M. and Cheung, T. D. and Marchese, P. and
   Kuznetsova, M. and Zheng, Y. and Chulaki, A. and Mohamed, A.},
Title = {A Model of an Integrated Research and Education Program in Space Weather
   at a Community College},
Journal = {SPACE WEATHER-THE INTERNATIONAL JOURNAL OF RESEARCH AND APPLICATIONS},
Year = {2020},
Volume = {18},
Number = {1},
Month = {JAN},
Abstract = {Community Colleges provide a great opportunity to diversify the space
   sciences or other science, technology, engineering, and math (STEM)
   fields due to their large population of underrepresented students.
   However, since the primary mission of community colleges is teaching,
   there is a challenge to support undergraduate research training and
   promote undergraduate research opportunities. Undergraduate research
   experiences are one of the leading high-impact practices (HIPs) to
   encourage students to pursue STEM majors, graduate degrees, and careers.
   Space weather provides the opportunity to engage undergraduate students
   in real-world research due to the accessibility of space mission data
   sets within open access data repositories. Space weather's impact on
   Earth's geospace environment, life, and society also provides a
   compelling real-world hook to engage students in activities that have a
   number of impacts including (1) long-term integration of space weather
   into the undergraduate curricula; (2) experience in analyzing large
   geospace data sets, which increases students' computational, critical
   thinking, and analytical skills, useful for any career; and (3) increase
   in students' interest in and motivation to study STEM, as well as
   preparing them for choosing a career path in space science and related
   fields. The model presented below has the potential to increase the
   retention, graduation, and transfer rate of community college students
   to four-year STEM programs, as well as increase representation and
   inclusion in space sciences and other related STEM fields.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Damas, MC (Corresponding Author), CUNY Queensborough Community Coll, Bayside, NY 11364 USA.
   Damas, M. C.; Cheung, T. D.; Marchese, P., CUNY Queensborough Community Coll, Bayside, NY 11364 USA.
   Ngwira, C. M., Atmospher \& Space Technol Res Associates, Boulder, CO USA.
   Ngwira, C. M., Catholic Univ Amer, Washington, DC 20064 USA.
   Ngwira, C. M., NASA, Goddard Space Flight Ctr, Washington, DC 20546 USA.
   Kuznetsova, M.; Zheng, Y.; Chulaki, A., NASA, Goddard Space Flight Ctr, Greenbelt, MD USA.
   Mohamed, A., CUNY, City Coll New York, New York, NY 10021 USA.},
DOI = {10.1029/2019SW002307},
Article-Number = {e2019SW002307},
EISSN = {1542-7390},
Keywords-Plus = {UNDERGRADUATE RESEARCH; STUDENTS; PARTNERSHIPS; EXPERIENCES; SCIENTISTS;
   GAINS},
Research-Areas = {Astronomy \& Astrophysics; Geochemistry \& Geophysics; Meteorology \&
   Atmospheric Sciences},
Web-of-Science-Categories  = {Astronomy \& Astrophysics; Geochemistry \& Geophysics; Meteorology \&
   Atmospheric Sciences},
Author-Email = {mdamas@qcc.cuny.edu},
Affiliations = {City University of New York (CUNY) System; Catholic University of
   America; National Aeronautics \& Space Administration (NASA); NASA
   Goddard Space Flight Center; National Aeronautics \& Space
   Administration (NASA); NASA Goddard Space Flight Center; City University
   of New York (CUNY) System; City College of New York (CUNY)},
ResearcherID-Numbers = {ngwira, chigomezyo M/D-7310-2012
   Zheng, Yihua/D-7368-2012
   },
ORCID-Numbers = {Kuznetsova, Maria/0009-0003-2524-1409
   Zheng, Yihua/0000-0002-2569-2950},
Funding-Acknowledgement = {NASA MUREP Community College Curriculum Improvement (MC3I) under NASA
   award {[}NNX15AV96A]; National Science Foundation Geosciences
   Directorate under NSF {[}DES-1446704]; CUNY Medgar Evers College NSF
   Research Experience for Undergraduates program; CUNY Research Scholars
   Program; NSF {[}AGS-1926022]},
Funding-Text = {This work was supported by grants from the NASA MUREP Community College
   Curriculum Improvement (MC3I) under NASA award NNX15AV96A and the
   National Science Foundation Geosciences Directorate under NSF award
   DES-1446704. The program also received partial funding for QCC students
   from several CUNY programs, including CUNY Medgar Evers College NSF
   Research Experience for Undergraduates program and the CUNY Research
   Scholars Program, C. M. Ngwira was also partially supported via NSF
   grant AGS-1926022 to ASTRA. M.C. Damas and all student participants
   express their sincerest thanks and gratitude to all mentors for their
   time, experience, and extraordinary support, especially Roger
   Dorsinville, Leon Johnson and CCMC staff. The authors also express their
   sincerest thanks and gratitude to the reviewers for their time. Special
   thanks to the many open data depositories, including the NASA Goddard
   Space Flight Center Data Facility (CDAWeb), NOAA SWPC, MADRIGAL, and
   Intermagnet. The authors have no data to declare.},
Number-of-Cited-References = {42},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Space Weather},
Doc-Delivery-Number = {KV0TP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000520137900006},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000505143700010,
Author = {Esch, Thomas and Asamer, Hubert and Bachofer, Felix and Balhar, Jakub
   and Boettcher, Martin and Boissier, Enguerran and d'Angelo, Pablo and
   Gevaert, Caroline M. and Hirner, Andreas and Jupova, Katerina and Kurz,
   Franz and Kwarteng, Andy Yaw and Mathot, Emmanuel and Marconcini, Mattia
   and Marin, Alessandro and Metz-Marconcini, Annekatrin and Pacini,
   Fabrizio and Paganini, Marc and Permana, Hans and Soukup, Tomas and
   Uereyen, Soner and Small, Christopher and Svaton, Vaclav and Zeidler,
   Julian Nils},
Title = {Digital world meets urban planet - new prospects for evidence-based
   urban studies arising from joint exploitation of big earth data,
   information technology and shared knowledge},
Journal = {INTERNATIONAL JOURNAL OF DIGITAL EARTH},
Year = {2020},
Volume = {13},
Number = {1, SI},
Pages = {136-157},
Month = {JAN 2},
Abstract = {The digital transformation taking place in all areas of life has led to
   a massive increase in digital data - in particular, related to the
   places where and the ways how we live. To facilitate an exploration of
   the new opportunities arising from this development the Urban Thematic
   Exploitation Platform (U-TEP) has been set-up. This enabling instrument
   represents a virtual environment that combines open access to
   multi-source data repositories with dedicated data processing, analysis
   and visualisation functionalities. Moreover, it includes mechanisms for
   the development and sharing of technology and knowledge. After an
   introduction of the underlying methodical concept, this paper introduces
   four selected use cases that were carried out on the basis of U-TEP: two
   technology-driven applications implemented by users from the remote
   sensing and software engineering community (generation of cloud-free
   mosaics, processing of drone data) and two examples related to concrete
   use scenarios defined by planners and decision makers (data analytics
   related to global urbanization, monitoring of regional land-use
   dynamics). The experiences from U-TEP's pre-operations phase show that
   the system can effectively support the derivation of new data, facts and
   empirical evidence that helps scientists and decision-makers to
   implement improved strategies for sustainable urban development.},
Publisher = {TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Esch, T (Corresponding Author), German Aerosp Ctr DLR, German Remote Sensing Data Ctr DFD, D-82234 Wessling, Germany.
   Esch, Thomas; Asamer, Hubert; Bachofer, Felix; d'Angelo, Pablo; Hirner, Andreas; Kurz, Franz; Marconcini, Mattia; Metz-Marconcini, Annekatrin; Uereyen, Soner; Zeidler, Julian Nils, German Aerosp Ctr DLR, German Remote Sensing Data Ctr DFD, D-82234 Wessling, Germany.
   Balhar, Jakub; Jupova, Katerina; Soukup, Tomas, GISAT Sro, Prague, Czech Republic.
   Boettcher, Martin; Permana, Hans, Brockmann Consult GmbH, Geesthacht, Germany.
   Boissier, Enguerran; Pacini, Fabrizio, Terradue Srl, Rome, Italy.
   Gevaert, Caroline M., Univ Twente, Int Inst Geoinformat Sci \& Earth Observat ICT, Enschede, Netherlands.
   Kwarteng, Andy Yaw, Sultan Qaboos Univ, Remote Sensing \& GIS Ctr, Muscat, Oman.
   Mathot, Emmanuel, Terradue Srl, Rome, Italy.
   Marin, Alessandro; Paganini, Marc, ESA, Frascati, Italy.
   Small, Christopher, Columbia Univ, Lamont Doherty Earth Observ, Dept Earth \& Environm Sci, New York, NY USA.
   Svaton, Vaclav, VSB Tech Univ Ostrava, IT4Innovat, Ostrava, Czech Republic.},
DOI = {10.1080/17538947.2018.1548655},
ISSN = {1753-8947},
EISSN = {1753-8955},
Keywords = {Service platform; urban; human settlements; earth observation; decision
   support},
Keywords-Plus = {URBANIZATION; SPACE; FRAMEWORK; CLIMATE; GROWTH; TIME},
Research-Areas = {Physical Geography; Remote Sensing},
Web-of-Science-Categories  = {Geography, Physical; Remote Sensing},
Author-Email = {Thomas.esch@dlr.de},
Affiliations = {Helmholtz Association; German Aerospace Centre (DLR); University of
   Twente; Sultan Qaboos University; Columbia University; Technical
   University of Ostrava},
ResearcherID-Numbers = {Bachofer, Felix/AAH-1648-2020
   Gevaert, Caroline/H-6195-2019
   Kwarteng, Andy Yaw/JPX-8844-2023
   },
ORCID-Numbers = {Bachofer, Felix/0000-0001-6181-0187
   Gevaert, Caroline/0000-0002-3983-2459
   Kwarteng, Andy Yaw/0000-0001-7929-458X
   Svaton, Vaclav/0000-0001-8187-8218
   Metz-Marconcini, Annekatrin/0009-0002-3896-4705},
Number-of-Cited-References = {51},
Times-Cited = {15},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {46},
Journal-ISO = {Int. J. Digit. Earth},
Doc-Delivery-Number = {JZ5LR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000505143700010},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000785076300001,
Author = {Lim, Hendrick Gao-Min and Hsiao, Shih-Hsin and Fann, Yang C. and Lee,
   Yuan-Chii Gladys},
Title = {Robust Mutation Profiling of SARS-CoV-2 Variants from Multiple Raw
   Illumina Sequencing Data with Cloud Workflow},
Journal = {GENES},
Year = {2022},
Volume = {13},
Number = {4},
Month = {APR},
Abstract = {Several variants of the novel severe acute respiratory syndrome
   coronavirus 2 (SARS-CoV-2) are emerging all over the world. Variant
   surveillance from genome sequencing has become crucial to determine if
   mutations in these variants are rendering the virus more infectious,
   potent, or resistant to existing vaccines and therapeutics. Meanwhile,
   analyzing many raw sequencing data repeatedly with currently available
   code-based bioinformatics tools is tremendously challenging to be
   implemented in this unprecedented pandemic time due to the fact of
   limited experts and computational resources. Therefore, in order to
   hasten variant surveillance efforts, we developed an installation-free
   cloud workflow for robust mutation profiling of SARS-CoV-2 variants from
   multiple Illumina sequencing data. Herein, 55 raw sequencing data
   representing four early SARS-CoV-2 variants of concern (Alpha, Beta,
   Gamma, and Delta) from an open-access database were used to test our
   workflow performance. As a result, our workflow could automatically
   identify mutated sites of the variants along with reliable annotation of
   the protein-coding genes at cost-effective and timely manner for all by
   harnessing parallel cloud computing in one execution under
   resource-limitation settings. In addition, our workflow can also
   generate a consensus genome sequence which can be shared with others in
   public data repositories to support global variant surveillance efforts.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Lee, YCG (Corresponding Author), Taipei Med Univ, Coll Med Sci \& Technol, Grad Inst Biomed Informat, Taipei 11031, Taiwan.
   Lim, Hendrick Gao-Min; Lee, Yuan-Chii Gladys, Taipei Med Univ, Coll Med Sci \& Technol, Grad Inst Biomed Informat, Taipei 11031, Taiwan.
   Hsiao, Shih-Hsin, Taipei Med Univ, Coll Med, Sch Med, Dept Internal Med,Div Pulm Med, Taipei 11031, Taiwan.
   Hsiao, Shih-Hsin, Taipei Med Univ Hosp, Dept Internal Med, Div Pulm Med, Taipei 11031, Taiwan.
   Fann, Yang C., NINDS, IT \& Bioinformat Program, Div Intramural, NIH, Bethesda, MD 20892 USA.},
DOI = {10.3390/genes13040686},
Article-Number = {686},
EISSN = {2073-4425},
Keywords = {COVID-19; SARS-CoV-2; mutation; variant; lineage; Illumina sequencing;
   cloud workflow; Common Workflow Language; parallel computing; genomics
   surveillance},
Research-Areas = {Genetics \& Heredity},
Web-of-Science-Categories  = {Genetics \& Heredity},
Author-Email = {hendrick.san@gmail.com
   hsiaomd@gmail.com
   fann@ninds.nih.gov
   ycgl@tmu.edu.tw},
Affiliations = {Taipei Medical University; Taipei Medical University; Taipei Medical
   University; Taipei Medical University Hospital; National Institutes of
   Health (NIH) - USA; NIH National Institute of Neurological Disorders \&
   Stroke (NINDS)},
ORCID-Numbers = {Lee, Yuan-Chii G./0000-0002-5074-7941
   Lim, Hendrick Gao-Min/0000-0002-7963-4174},
Funding-Acknowledgement = {Ministry of Science and Technology (MOST) of the Taiwanese government
   {[}MOST 109-2221-E-038-016]; Taipei Medical University Hospital
   {[}W0303, 109TMUH-SP-02]; Division of Intramural Research Program,
   National Institute of Neurological Disorders and Stroke, National
   Institutes of Health, USA; National Cancer Institute, National
   Institutes of Health {[}HHSN261201400008C, 17x146, HHSN261201500003I,
   75N91019D00024]},
Funding-Text = {This work was supported in part by the Ministry of Science and
   Technology (MOST) (grant MOST 109-2221-E-038-016) of the Taiwanese
   government to Y.-C.G.L., the Taipei Medical University Hospital (W0303,
   109TMUH-SP-02) to S.-H.H. and the Fund from the Division of Intramural
   Research Program, National Institute of Neurological Disorders and
   Stroke, National Institutes of Health, USA to Y.C.F. The Seven Bridges
   Cancer Research Data Commons Cloud Resource has been funded in whole or
   in part with federal funds from the National Cancer Institute, National
   Institutes of Health (Contract No. HHSN261201400008C and ID/IQ Agreement
   No. 17x146 under Contract No. HHSN261201500003I and 75N91019D00024).},
Number-of-Cited-References = {53},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Genes},
Doc-Delivery-Number = {0Q7EE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000785076300001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000371444500005,
Author = {Li, Simon and Besson, Sebastien and Blackburn, Colin and Carroll, Mark
   and Ferguson, Richard K. and Flynn, Helen and Gillen, Kenneth and Leigh,
   Roger and Lindner, Dominik and Linkert, Melissa and Moore, William J.
   and Ramalingam, Balaji and Rozbicki, Emil and Rustici, Gabriella and
   Tarkowska, Aleksandra and Walczysko, Petr and Williams, Eleanor and
   Allan, Chris and Burel, Jean-Marie and Moore, Josh and Swedlow, Jason R.},
Title = {Metadata management for high content screening in OMERO},
Journal = {METHODS},
Year = {2016},
Volume = {96},
Pages = {27-32},
Month = {MAR 1},
Abstract = {High content screening (HCS) experiments create a classic data
   management challenge multiple, large sets of heterogeneous structured
   and unstructured data, that must be integrated and linked to produce a
   set of ``final{''} results. These different data include images,
   reagents, protocols, analytic output, and phenotypes, all of which must
   be stored, linked and made accessible for users, scientists,
   collaborators and where appropriate the wider community. The OME
   Consortium has built several open source tools for managing, linking and
   sharing these different types of data. The OME Data Model is a metadata
   specification that supports the image data and metadata recorded in HCS
   experiments. Bio-Formats is a Java library that reads recorded image
   data and metadata and includes support for several HCS screening
   systems. OMERO is an enterprise data management application that
   integrates image data, experimental and analytic metadata and makes them
   accessible for visualization, mining, sharing and downstream analysis.
   We discuss how Bio-Formats and OMERO handle these different data types,
   and how they can be used to integrate, link and share HCS experiments in
   facilities and public data repositories. OME specifications and software
   are open source and are available at https://www.openmicroscopy.org. (C)
   2015 The Authors. Published by Elsevier Inc. This is an open access
   article under the CC BY license.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Swedlow, JR (Corresponding Author), Univ Dundee, Ctr Gene Regulat \& Express, Dundee, Scotland.
   Li, Simon; Besson, Sebastien; Blackburn, Colin; Carroll, Mark; Ferguson, Richard K.; Flynn, Helen; Gillen, Kenneth; Leigh, Roger; Lindner, Dominik; Moore, William J.; Ramalingam, Balaji; Rustici, Gabriella; Tarkowska, Aleksandra; Walczysko, Petr; Williams, Eleanor; Burel, Jean-Marie; Moore, Josh; Swedlow, Jason R., Univ Dundee, Ctr Gene Regulat \& Express, Dundee, Scotland.
   Linkert, Melissa; Rozbicki, Emil; Allan, Chris; Moore, Josh; Swedlow, Jason R., Glencoe Software Inc, Seattle, WA USA.},
DOI = {10.1016/j.ymeth.2015.10.006},
ISSN = {1046-2023},
EISSN = {1095-9130},
Keywords = {Data management; Screening; Metadata; HCS},
Keywords-Plus = {QUANTITATIVE-ANALYSIS; HUMAN GENOME; OPEN TOOLS; IMAGE DATA; MICROSCOPY;
   REVEALS; MODEL; ORGANIZATION; INFORMATICS; PROTEINS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Biochemistry \& Molecular Biology},
Author-Email = {jrswedlow@dundee.ac.uk},
Affiliations = {University of Dundee},
ResearcherID-Numbers = {Williams, Eleanor/JKJ-6665-2023
   Moore, Joshua Allen/IXD-9732-2023
   },
ORCID-Numbers = {Moore, Joshua Allen/0000-0003-4028-811X
   Ferguson, Gus/0000-0003-1567-270X
   Allan, Chris/0000-0002-8151-4059
   Lindner, Dominik/0000-0001-8038-1250
   Tarkowska, Aleksandra/0000-0002-3392-3691
   Flynn, Helen/0000-0001-6393-8942
   Besson, Sebastien/0000-0001-8783-1429
   Moore, William/0000-0002-7264-8338
   Swedlow, Jason/0000-0002-2198-1958
   Williams, Eleanor/0000-0002-0851-7990
   Rustici, Gabriella/0000-0003-3085-1271
   Li, Simon/0000-0002-7929-2442
   Gillen, Kenneth/0000-0001-6104-6190},
Funding-Acknowledgement = {Wellcome Trust Strategic Award {[}095931/Z/11/Z]; BBSRC BBR awards
   {[}BB/L024233/1, BB/M018423/1]; Biotechnology and Biological Sciences
   Research Council {[}BB/M018423/1, BB/L024233/1] Funding Source:
   researchfish; BBSRC {[}BB/M018423/1, BB/L024233/1] Funding Source: UKRI;
   Wellcome Trust {[}095931/Z/11/Z] Funding Source: Wellcome Trust},
Funding-Text = {The authors thank all the Bio-Formats and OMERO user community for
   helpful feedback and suggestions for improvements to OME software. This
   work was supported by a Wellcome Trust Strategic Award (095931/Z/11/Z)
   and two BBSRC BBR awards (BB/L024233/1 and BB/M018423/1).},
Number-of-Cited-References = {34},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Methods},
Doc-Delivery-Number = {DF6CX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000371444500005},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000377352000001,
Author = {Mehmood, Nadeem Qaisar and Culmone, Rosario and Mostarda, Leonardo},
Title = {A Flexible and Scalable Architecture for Real-Time ANT plus Sensor Data
   Acquisition and NoSQL Storage},
Journal = {INTERNATIONAL JOURNAL OF DISTRIBUTED SENSOR NETWORKS},
Year = {2016},
Abstract = {Wireless Personal or Body Area Networks (WPANs or WBANs) are the main
   mechanisms to develop healthcare systems for an ageing society. Such
   systems offer monitoring, security, and caring services by measuring
   physiological body parameters using wearable devices. Wireless sensor
   networks allow inexpensive, continuous, and real-time updates of the
   sensor data, to the data repositories via an Internet. A great deal of
   research is going on with a focus on technical, managerial, economic,
   and social health issues. The technical obstacles, which we encounter,
   in general, are better methodologies, architectures, and context data
   storage. Sensor communication, data processing and interpretation, data
   interchange format, data transferal, and context data storage are
   sensitive phases during the whole process of body parameter acquisition
   until the storage. ANT+ is a proprietary (but open access) low energy
   protocol, which supports device interoperability by mutually agreeing
   upon device profile standards. We have implemented a prototype, based
   upon ANT+ enabled sensors for a real-time scenario. This paper presents
   a system architecture, with its software organization, for real-time
   message interpretation, event-driven based real-time bidirectional
   communication, and schema flexible storage. A computer user uses it to
   acquire and to transmit the data using a Windows service to the context
   server.},
Publisher = {SAGE PUBLICATIONS INC},
Address = {2455 TELLER RD, THOUSAND OAKS, CA 91320 USA},
Type = {Article},
Language = {English},
Affiliation = {Mehmood, NQ (Corresponding Author), Univ Camerino, Dept Comp Sci, I-62032 Camerino, Italy.
   Mehmood, Nadeem Qaisar; Culmone, Rosario; Mostarda, Leonardo, Univ Camerino, Dept Comp Sci, I-62032 Camerino, Italy.},
DOI = {10.1155/2016/3651591},
Article-Number = {3651591},
ISSN = {1550-1477},
Keywords-Plus = {NETWORKS},
Research-Areas = {Computer Science; Telecommunications},
Web-of-Science-Categories  = {Computer Science, Information Systems; Telecommunications},
Author-Email = {nadeemqaisar.mehmood@unicam.it},
Affiliations = {University of Camerino},
ResearcherID-Numbers = {mostarda, leonardo/AAG-9295-2020
   Mehmood, Nadeem Qaisar/IAQ-3469-2023},
ORCID-Numbers = {mostarda, leonardo/0000-0001-8852-8317
   Culmone, Rosario/0000-0003-3333-0893
   Mehmood, Nadeem Qaisar/0000-0001-9928-4637},
Funding-Acknowledgement = {Software Industry; Ministry of Education; University and Research, Italy},
Funding-Text = {This work is part of the EUREKA (XXVIII Cycle) project which results
   from the cooperation between Servili Computers s.r.l., Italy; the
   University of Camerino (Department of Computer Science), Italy; and the
   state department Regione Marche, Italy. The authors thank the Software
   Industry; Ministry of Education; University and Research, Italy, for the
   financial support of this project.},
Number-of-Cited-References = {80},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Int. J. Distrib. Sens. Netw.},
Doc-Delivery-Number = {DN8TI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000377352000001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000604388400011,
Author = {Khan, Saad M. and Liu, Xiaoxuan and Nath, Siddharth and Korot, Edward
   and Faes, Livia and Wagner, Siegfried K. and Keane, Pearse A. and
   Sebire, Neil J. and Burton, Matthew J. and Denniston, Alastair K.},
Title = {A global review of publicly available datasets for ophthalmological
   imaging: barriers to access, usability, and generalisability},
Journal = {LANCET DIGITAL HEALTH},
Year = {2021},
Volume = {3},
Number = {1},
Pages = {E51-E66},
Month = {JAN},
Abstract = {Health data that are publicly available are valuable resources for
   digital health research. Several public datasets containing
   ophthalmological imaging have been frequently used in machine learning
   research; however, the total number of datasets containing
   ophthalmological health information and their respective content is
   unclear. This Review aimed to identify all publicly available
   ophthalmological imaging datasets, detail their accessibility, describe
   which diseases and populations are represented, and report on the
   completeness of the associated metadata. With the use of MEDLINE,
   Google's search engine, and Google Dataset Search, we identified 94 open
   access datasets containing 507 724 images and 125 videos from 122 364
   patients. Most datasets originated from Asia, North America, and Europe.
   Disease populations were unevenly represented, with glaucoma, diabetic
   retinopathy, and age-related macular degeneration disproportionately
   overrepresented in comparison with other eye diseases. The reporting of
   basic demographic characteristics such as age, sex, and ethnicity was
   poor, even at the aggregate level. This Review provides greater
   visibility for ophthalmological datasets that are publicly available as
   powerful resources for research. Our paper also exposes an increasing
   divide in the representation of different population and disease groups
   in health data repositories. The improved reporting of metadata would
   enable researchers to access the most appropriate datasets for their
   needs and maximise the potential of such resources.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Review},
Language = {English},
Affiliation = {Denniston, AK (Corresponding Author), Univ Birmingham, Acad Unit Ophthalmol, Inst Inflammat \& Ageing, Coll Med \& Dent Sci, Birmingham B15 2TT, W Midlands, England.
   Khan, Saad M.; Liu, Xiaoxuan; Denniston, Alastair K., Univ Birmingham, Acad Unit Ophthalmol, Inst Inflammat \& Ageing, Coll Med \& Dent Sci, Birmingham B15 2TT, W Midlands, England.
   Liu, Xiaoxuan; Denniston, Alastair K., Univ Hosp Birmingham NHS Fdn Trust, Dept Ophthalmol, Birmingham, W Midlands, England.
   Liu, Xiaoxuan; Korot, Edward; Faes, Livia, Moorfields Eye Hosp NHS Fdn Trust, London, England.
   Liu, Xiaoxuan; Sebire, Neil J.; Denniston, Alastair K., Hlth Data Res UK, London, England.
   Liu, Xiaoxuan; Denniston, Alastair K., Birmingham Hlth Partners, Ctr Regulatory Sci \& Innovat, Birmingham, W Midlands, England.
   Nath, Siddharth, McGill Univ, Dept Ophthalmol \& Visual Sci, Montreal, PQ, Canada.
   Korot, Edward, Stanford Univ, Byers Eye Inst, Palo Alto, CA 94304 USA.
   Faes, Livia, Cantonal Hosp Lucerne, Eye Clin, Luzern, Switzerland.
   Wagner, Siegfried K.; Keane, Pearse A.; Denniston, Alastair K., Moorfields Eye Hosp NHS Fdn Trust, Natl Inst Hlth Res, Biomed Res Ctr Ophthalmol, London, England.
   Wagner, Siegfried K.; Keane, Pearse A.; Denniston, Alastair K., UCL Inst Ophthalmol, London, England.
   Burton, Matthew J., London Sch Hyg \& Trop Med, Int Ctr Eye Hlth, Dept Clin Res, London, England.},
DOI = {10.1016/S2589-7500(20)30240-5},
EISSN = {2589-7500},
Keywords-Plus = {DIABETIC-RETINOPATHY; DISEASES; CANCER; SYSTEM},
Research-Areas = {Medical Informatics; General \& Internal Medicine},
Web-of-Science-Categories  = {Medical Informatics; Medicine, General \& Internal},
Author-Email = {a.denniston@bham.ac.uk},
Affiliations = {University of Birmingham; University of Birmingham; University of
   London; University College London; Moorfields Eye Hospital NHS
   Foundation Trust; McGill University; Stanford University; Lucerne
   Cantonal Hospital; University of London; University College London;
   Moorfields Eye Hospital NHS Foundation Trust; University of London;
   University College London; University of London; London School of
   Hygiene \& Tropical Medicine},
ResearcherID-Numbers = {Denniston, Alastair/ABD-1238-2020
   Wagner, Siegfried Karl/HNR-9338-2023
   },
ORCID-Numbers = {Denniston, Alastair/0000-0001-7849-0087
   Keane, Pearse/0000-0002-9239-745X
   Burton, Matthew/0000-0003-1872-9169
   Sebire, Neil/0000-0001-5348-9063
   Korot, Edward/0000-0002-5687-1564
   Liu, Xiaoxuan/0000-0002-1286-0038},
Funding-Acknowledgement = {Queen Elizabeth Diamond Jubilee Trust; Moorfields Eye Charity
   {[}GR001061]; National Institute for Health Research Moorfields
   Biomedical Research Centre; Wellcome Trust; Sightsavers; Fred Hollows
   Foundation; British Council for the Prevention of Blindness; Christian
   Blind Mission; SEVA Foundation},
Funding-Text = {The Lancet Global Health Commission on Global Eye Health is supported by
   The Queen Elizabeth Diamond Jubilee Trust, Moorfields Eye Charity (grant
   no. GR001061), National Institute for Health Research Moorfields
   Biomedical Research Centre, The Wellcome Trust, Sightsavers, The Fred
   Hollows Foundation, The SEVA Foundation, The British Council for the
   Prevention of Blindness, and Christian Blind Mission.},
Number-of-Cited-References = {37},
Times-Cited = {103},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Lancet Digit. Health},
Doc-Delivery-Number = {PN3NE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000604388400011},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000306887400003,
Author = {Bates, Timothy C. and Lewis, Gary J.},
Title = {Towards a genetically informed approach in the social sciences:
   Strengths and an opportunity},
Journal = {PERSONALITY AND INDIVIDUAL DIFFERENCES},
Year = {2012},
Volume = {53},
Number = {4, SI},
Pages = {374-380},
Month = {SEP},
Abstract = {Researchers agree that heritable effects influence almost all traits of
   interest for social science. A corollary of ubiquitous heritability is
   that measurement and control of genetic differences is essential for
   basic and applied social science. Despite this, remarkably few studies
   in the social sciences use genetically informative samples. Here we
   discuss how complex-trait behavior genetics can be used more effectively
   to address a range of social science questions, including multivariate
   genetic modeling, discordant twin designs, studies of gene-environment
   interaction, and adoption studies. We next advocate a concerted effort
   to build a new openly accessible resource to increase the utilization of
   genetically informative designs in social science research. Specific
   criteria for this proposed resource are defined and include full
   coverage of socio-economic status, multiple and complementary family,
   environmental, and genetic relationships, an open and extensible method
   for low-cost testing, and an open-access data repository. We suggest the
   cost would be moderate and returns high, generating benefits for many
   hundreds of researchers, maximizing impact for funders, and increase the
   rate of scientific progress in social science. (C) 2012 Elsevier Ltd.
   All rights reserved.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bates, TC (Corresponding Author), Univ Edinburgh, Dept Psychol, 7 George Sq, Edinburgh EH8 9JZ, Midlothian, Scotland.
   Bates, Timothy C., Univ Edinburgh, Dept Psychol, Edinburgh EH8 9JZ, Midlothian, Scotland.
   Bates, Timothy C., Univ Edinburgh, Ctr Cognit Epidemiol \& Cognit Ageing, Edinburgh EH8 9JZ, Midlothian, Scotland.
   Lewis, Gary J., Univ Calif Santa Barbara, Sage Ctr Study Mind, Dept Psychol \& Brain Sci, Santa Barbara, CA 93106 USA.},
DOI = {10.1016/j.paid.2012.03.002},
ISSN = {0191-8869},
EISSN = {1873-3549},
Keywords = {Behavior genetics; Twins; Open-source; Reverse causation; Causal
   hypotheses; Confounding; Social psychology; Shared environment},
Keywords-Plus = {CULTURAL TRANSMISSION; SHARED ENVIRONMENT; REGULAR EXERCISE; TWIN;
   CAUSALITY; ANXIETY; FAMILY; HERITABILITY; INTELLIGENCE; DEPRESSION},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Social},
Author-Email = {tim.bates@ed.ac.uk
   glewis1@gmail.com},
Affiliations = {University of Edinburgh; University of Edinburgh; University of
   California System; University of California Santa Barbara},
ResearcherID-Numbers = {Bates, Timothy C/C-9637-2010},
ORCID-Numbers = {Bates, Timothy C/0000-0002-1153-9007},
Number-of-Cited-References = {58},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {12},
Journal-ISO = {Pers. Individ. Differ.},
Doc-Delivery-Number = {980IS},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000306887400003},
DA = {2024-01-15},
}

@article{ WOS:001034560100005,
Author = {Cuper-Przybylska, Dominika and Nguyen, Van Nhanh and Nam, Cao Dao and
   Kowalski, Jerzy},
Title = {HIGH QUALITY MULTI-ZONE AND 3D CFD MODEL OF COMBUSTION IN MARINE DIESEL
   ENGINE CYLINDER},
Journal = {POLISH MARITIME RESEARCH},
Year = {2023},
Volume = {30},
Number = {2},
Pages = {61-67},
Month = {JUN 1},
Abstract = {The paper presents a 3D model of the processes taking place in the
   cylinder of a large 4-stroke marine engine. The model is based on CFD
   calculations performed on the moving mesh. The modelling range includes
   the full duty cycle (720 degrees crankshaft position) and the complete
   geometry of the cylinder with inlet and exhaust ducts. The input data,
   boundary conditions and validation data were obtained by direct
   measurements on the real object. Fuel injection characteristics were
   obtained by Mie scattering measurements in a fixed-volume chamber. The
   modelling results have been validated in terms of the pressure
   characteristics of the engine's cylinder within the entire range of its
   loads. The mean error did not exceed 1.42\% for the maximum combustion
   pressure and 1.13\% for the MIP (Mean Indicated Pressure). The model was
   also positively validated in terms of the O-2 and NOx content of the
   exhaust gas. The mean error in this case was 1.2\% for NOx fractions in
   the exhaust gas and 0.4\% for O-2 fractions. The complete model data has
   been made available in the research data repository on an open access
   basis.},
Publisher = {SCIENDO},
Address = {BOGUMILA ZUGA 32A, WARSAW, MAZOVIA, POLAND},
Type = {Article},
Language = {English},
Affiliation = {Kowalski, J (Corresponding Author), Gdansk Univ Technol, Gdansk, Poland.
   Cuper-Przybylska, Dominika, Cent Off Measures POLAND, Warsaw, Poland.
   Nguyen, Van Nhanh, HUTECH Univ, Inst Engn, Ho Chi Minh City, Vietnam.
   Nam, Cao Dao, Ho Chi Minh City Univ Transport, Inst Mech Engn, Ho Chi Minh City, Vietnam.
   Kowalski, Jerzy, Gdansk Univ Technol, Gdansk, Poland.},
DOI = {10.2478/pomr-2023-0021},
ISSN = {1233-2585},
EISSN = {2083-7429},
Keywords = {CFD combustion model; large 4-stroke engine; diesel engine; emission;
   NOx concentration},
Keywords-Plus = {EMISSIONS; PERFORMANCE; PREDICTION; PRESSURE; EXHAUST; FLOW; EGR},
Research-Areas = {Engineering},
Web-of-Science-Categories  = {Engineering, Marine},
Author-Email = {jerzy.kowalski@pg.edu.pl},
Affiliations = {Ho Chi Minh City University of Technology (HUTECH); Vietnam National
   University Hochiminh City; Ho Chi Minh City University of Transport;
   Fahrenheit Universities; Gdansk University of Technology},
ORCID-Numbers = {Jerzy, Kowalski/0000-0002-2764-3765
   Van Nhanh, Nguyen/0000-0003-4241-3359
   Cao, Dao Nam/0000-0002-4641-8563},
Funding-Acknowledgement = {AVL},
Funding-Text = {The work was supported by AVL, the FIRE software developer, under the
   ``University Partnership{''} affiliate program.},
Number-of-Cited-References = {44},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Pol. Marit. Res.},
Doc-Delivery-Number = {N1FQ9},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001034560100005},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000481446600005,
Author = {Bocquier, Philippe and Ginsburg, Carren and Collinson, Mark A.},
Title = {A training manual for event history analysis using longitudinal data},
Journal = {BMC RESEARCH NOTES},
Year = {2019},
Volume = {12},
Number = {1},
Month = {AUG 14},
Abstract = {Objective This research note reports on the activities of the
   Multi-centre Analysis of the Dynamics of Internal Migration And Health
   (MADIMAH) project aimed at collating and testing of a set of tools to
   conduct longitudinal event history analyses applied to standardised
   Health and Demographic Surveillance System (HDSS) datasets. The methods
   are illustrated using an example of longitudinal micro-data from the
   Agincourt HDSS, one of a number of open access datasets available
   through the INDEPTH iShare2 data repository. The research note documents
   the experience of the MADIMAH group in analysing HDSS data and
   demonstrates how complex analyses can be streamlined and conducted in an
   accessible way. These tools are aimed at aiding analysts and researchers
   wishing to conduct longitudinal data analysis of demographic events.
   Results The methods demonstrated in this research note may successfully
   be applied by practitioners to longitudinal micro-data from HDSS, as
   well as retrospective surveys or register data. The illustrations
   provided are accompanied by detailed, tested computer programs, which
   demonstrate the full potential of longitudinal data to generate both
   cross-sectional and longitudinal standard descriptive estimates as well
   as more complex regression estimates.},
Publisher = {SPRINGERNATURE},
Address = {CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bocquier, P (Corresponding Author), Catholic Univ Louvain, Ctr Rech Demog, Pl Montesquieu,1 Bte L2-08-03, B-1348 Louvain La Neuve, Belgium.
   Bocquier, P (Corresponding Author), Univ Witwatersrand, Fac Hlth Sci, Sch Publ Hlth, Med Res Council,Wits Rural Publ Hlth \& Hlth Trans, Johannesburg, South Africa.
   Bocquier, Philippe, Catholic Univ Louvain, Ctr Rech Demog, Pl Montesquieu,1 Bte L2-08-03, B-1348 Louvain La Neuve, Belgium.
   Bocquier, Philippe; Ginsburg, Carren; Collinson, Mark A., Univ Witwatersrand, Fac Hlth Sci, Sch Publ Hlth, Med Res Council,Wits Rural Publ Hlth \& Hlth Trans, Johannesburg, South Africa.
   Collinson, Mark A., South African Populat Res Infrastruct Network, Med Res Council, Dept Sci \& Technol, Johannesburg, South Africa.},
DOI = {10.1186/s13104-019-4544-1},
Article-Number = {506},
EISSN = {1756-0500},
Keywords = {Longitudinal data analysis; Demographic rates; Event history analysis;
   Health and Demographic Surveillance System},
Keywords-Plus = {DEMOGRAPHIC SURVEILLANCE SYSTEMS; HEALTH; MIGRATION},
Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Science \& Technology -
   Other Topics},
Web-of-Science-Categories  = {Biology; Multidisciplinary Sciences},
Author-Email = {philippe.bocquier@uclouvain.be},
Affiliations = {Universite Catholique Louvain; South African Medical Research Council;
   University of Witwatersrand; South African Medical Research Council},
ORCID-Numbers = {Bocquier, Philippe/0000-0002-6278-0597
   Ginsburg, Carren/0000-0002-8391-8268},
Funding-Acknowledgement = {Swedish International Development Agency {[}Sida: 2012-000379]; National
   Research Foundation, South Africa (Joint NRF-FNRS Grant) {[}95284];
   Wallonia-Brussels Federation of Belgium (Joint NRF-FNRS Grant)
   {[}95284]; Wallonia-Brussels Federation of Belgium grant (FNRS)
   {[}29137033]; South African Medical Research Council (SAMRC)},
Funding-Text = {The work on this research note and training manual forms part of the
   activities of the INDEPTH Multi-centre Analysis of the Dynamics of
   Internal Migration And Health (MADIMAH) project. The project has
   received funds from the Swedish International Development Agency (Sida:
   2012-000379) as well as joint financial support from the National
   Research Foundation, South Africa, and the Wallonia-Brussels Federation
   of Belgium (Joint NRF-FNRS Grant No: 95284). Further support was
   received from another Wallonia-Brussels Federation of Belgium grant
   (FNRS Grant No: 29137033). We gratefully acknowledge the South African
   Medical Research Council (SAMRC) for funding Carren Ginsburg's Career
   Development Award. None of the listed funding agencies interfered in the
   design of the study and collection, analysis, and interpretation of data
   and in writing the manuscript.},
Number-of-Cited-References = {13},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {BMC Res. Notes},
Doc-Delivery-Number = {IR5AY},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000481446600005},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000881704400001,
Author = {Maes, Hermine H. M. and Lapato, Dana M. and Schmitt, J. Eric and
   Luciana, Monica and Banich, Marie T. and Bjork, James M. and Hewitt,
   John K. and Madden, Pamela A. and Heath, Andrew C. and Barch, Deanna M.
   and Thompson, Wes K. and Iacono, William G. and Neale, Michael C.},
Title = {Genetic and Environmental Variation in Continuous Phenotypes in the ABCD
   Study®},
Journal = {BEHAVIOR GENETICS},
Year = {2023},
Volume = {53},
Number = {1},
Pages = {1-24},
Month = {FEB},
Abstract = {Twin studies yield valuable insights into the sources of variation,
   covariation and causation in human traits. The ABCD Study (R)
   (abcdstudy.org) was designed to take advantage of four universities
   known for their twin research, neuroimaging, population-based sampling,
   and expertise in genetic epidemiology so that representative twin
   studies could be performed. In this paper we use the twin data to: (i)
   provide initial estimates of heritability for the wide range of
   phenotypes assessed in the ABCD Study using a consistent direct variance
   estimation approach, assuring that both data and methodology are sound;
   and (ii) provide an online resource for researchers that can serve as a
   reference point for future behavior genetic studies of this publicly
   available dataset. Data were analyzed from 772 pairs of twins aged 9-10
   years at study inception, with zygosity determined using genotypic data,
   recruited and assessed at four twin hub sites. The online tool provides
   twin correlations and both standardized and unstandardized estimates of
   additive genetic, and environmental variation for 14,500 continuously
   distributed phenotypic features, including: structural and functional
   neuroimaging, neurocognition, personality, psychopathology, substance
   use propensity, physical, and environmental trait variables. The
   estimates were obtained using an unconstrained variance approach, so
   they can be incorporated directly into meta-analyses without upwardly
   biasing aggregate estimates. The results indicated broad consistency
   with prior literature where available and provided novel estimates for
   phenotypes without prior twin studies or those assessed at different
   ages. Effects of site, self-identified race/ethnicity, age and sex were
   statistically controlled. Results from genetic modeling of all 53,172
   continuous variables, including 38,672 functional MRI variables, will be
   accessible via the user-friendly open-access web interface we have
   established, and will be updated as new data are released from the ABCD
   Study. This paper provides an overview of the initial results from the
   twin study embedded within the ABCD Study, an introduction to the
   primary research domains in the ABCD study and twin methodology, and an
   evaluation of the initial findings with a focus on data quality and
   suitability for future behavior genetic studies using the ABCD dataset.
   The broad introductory material is provided in recognition of the
   multidisciplinary appeal of the ABCD Study. While this paper focuses on
   univariate analyses, we emphasize the opportunities for multivariate,
   developmental and causal analyses, as well as those evaluating
   heterogeneity by key moderators such as sex, demographic factors and
   genetic background.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Maes, HHM (Corresponding Author), Virginia Commonwealth Univ, Virginia Inst Psychiat \& Behav Genet, Dept Human \& Mol Genet, POB 980033, Richmond, VA 23298 USA.
   Maes, HHM (Corresponding Author), Virginia Commonwealth Univ, Virginia Inst Psychiat \& Behav Genet, Dept Psychiat, Richmond, VA 23284 USA.
   Maes, HHM (Corresponding Author), Virginia Commonwealth Univ, Massey Canc Ctr, Richmond, VA 23284 USA.
   Maes, Hermine H. M.; Lapato, Dana M.; Neale, Michael C., Virginia Commonwealth Univ, Virginia Inst Psychiat \& Behav Genet, Dept Human \& Mol Genet, POB 980033, Richmond, VA 23298 USA.
   Maes, Hermine H. M.; Bjork, James M.; Neale, Michael C., Virginia Commonwealth Univ, Virginia Inst Psychiat \& Behav Genet, Dept Psychiat, Richmond, VA 23284 USA.
   Maes, Hermine H. M., Virginia Commonwealth Univ, Massey Canc Ctr, Richmond, VA 23284 USA.
   Schmitt, J. Eric, Univ Penn, Dept Radiol, Philadelphia, PA 19104 USA.
   Schmitt, J. Eric, Univ Penn, Dept Psychiat, Philadelphia, PA 19104 USA.
   Luciana, Monica; Iacono, William G., Univ Minnesota, Dept Psychol, Minneapolis, MN USA.
   Banich, Marie T., Univ Colorado, Dept Psychol \& Neurosci, Boulder, CO 80309 USA.
   Banich, Marie T.; Hewitt, John K., Univ Colorado, Inst Cognit Sci, Boulder, CO 80309 USA.
   Hewitt, John K., Univ Colorado, Inst Behav Genet, Boulder, CO 80309 USA.
   Madden, Pamela A.; Heath, Andrew C.; Barch, Deanna M., Washington Univ, Dept Psychiat, St Louis, MO 63110 USA.
   Thompson, Wes K., Univ Calif San Diego, Populat Neurosci \& Genet Lab, Div Biostat, La Jolla, CA 92093 USA.
   Thompson, Wes K., Univ Calif San Diego, Populat Neurosci \& Genet Lab, Dept Radiol, La Jolla, CA 92093 USA.},
DOI = {10.1007/s10519-022-10123-w},
EarlyAccessDate = {NOV 2022},
ISSN = {0001-8244},
EISSN = {1573-3297},
Keywords = {ABCD; Adolescence; Twin; Heritability; Environment; Neuroscience;
   Genetics; Cognition; Cognitive abilities; Personality; Psychiatric
   disorders; Substance use; Children; Open science; FAIR data},
Keywords-Plus = {NIH TOOLBOX; WHITE-MATTER; INDIVIDUAL-DIFFERENCES; EXECUTIVE FUNCTIONS;
   CORTICAL THICKNESS; CHILDHOOD; CHILDREN; TWIN; HERITABILITY; STABILITY},
Research-Areas = {Behavioral Sciences; Genetics \& Heredity; Psychology},
Web-of-Science-Categories  = {Behavioral Sciences; Genetics \& Heredity; Psychology, Multidisciplinary},
Author-Email = {hmaes@vcu.edu},
Affiliations = {Virginia Commonwealth University; Virginia Commonwealth University;
   Virginia Commonwealth University; University of Pennsylvania; University
   of Pennsylvania; University of Minnesota System; University of Minnesota
   Twin Cities; University of Colorado System; University of Colorado
   Boulder; University of Colorado System; University of Colorado Boulder;
   University of Colorado System; University of Colorado Boulder;
   Washington University (WUSTL); University of California System;
   University of California San Diego; University of California System;
   University of California San Diego},
ResearcherID-Numbers = {Bjork, James/Q-5108-2019
   },
ORCID-Numbers = {Bjork, James/0000-0003-0593-3291
   Schmitt, James/0000-0002-7487-227X
   Maes, Hermine/0000-0001-7489-2214},
Funding-Acknowledgement = {National Institutes of Health {[}U01DA041022, U01DA041025, U01DA041028,
   U01DA041048, U01DA041089, U01DA041093, U01DA041106, U01DA041117,
   U01DA041120, U01DA041134]; NIH {[}U01DA041148, U01DA041156, U01DA041174,
   U24DA041123, U24DA041147, U01DA050987, U01DA050988, U01DA050989,
   U01DA051018, U01DA051037, U01DA051038, U01DA051039]},
Funding-Text = {Data used in the preparation of this article were obtained from the
   Adolescent Brain Cognitive Development (ABCD) Study (R)
   (https://abcdstudy.org), held in the NIMH Data Archive (NDA). This is a
   multisite, longitudinal study designed to recruit more than 10,000
   children age 9-10 and follow them over 10 years into early adulthood.
   The ABCD Study (R) is supported by the National Institutes of Health and
   additional federal partners under award numbers U01DA041022,
   U01DA041025, U01DA041028, U01DA041048, U01DA041089, U01DA041093,
   U01DA041106, U01DA041117, U01DA041120, U01DA041134, U01DA041148,
   U01DA041156, U01DA041174, U24DA041123, U24DA041147, U01DA050987,
   U01DA050988, U01DA050989, U01DA050988, U01DA051018,
   U01DA051037,U01DA051038, U01DA051039. A full list of supporters is
   available at https://abcdstudy.org/federal-partners.html.A listing of
   participating sites and a complete listing of the study investigators
   can be found at https://abcdstudy.org/scien tists/workgroups/. ABCD
   consortium investigators designed and implemented the study and/or
   provided data but did not necessarily participate in analysis or writing
   of this report. This manuscript reflects the views of the authors and
   may not reflect the opinions or views of the NIH or ABCD consortium
   investigators. The ABCD data repository grows and changes over time. The
   ABCD data used in this report came from
   {[}http://dx.doi.org/10.15154/1503209].},
Number-of-Cited-References = {100},
Times-Cited = {5},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Behav. Genet.},
Doc-Delivery-Number = {7R0KA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000881704400001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000522772100001,
Author = {Dumont, Julie R. and Salewski, Ryan and Beraldo, Flavio},
Title = {Critical mass: The rise of a touchscreen technology community for rodent
   cognitive testing},
Journal = {GENES BRAIN AND BEHAVIOR},
Year = {2021},
Volume = {20},
Number = {1},
Month = {JAN},
Abstract = {The rise in the number of users and institutions utilizing the rodent
   touchscreen technology for cognitive testing over the past decade has
   prompted the need for knowledge mobilization and community building. To
   address the needs of the growing touchscreen community, the first
   international touchscreen symposium was hosted at Western University.
   Attendees from around the world attended talks from expert
   neuroscientists using touchscreens to examine a vast array of questions
   regarding cognition and the nervous system. In addition to the
   symposium, a subset of attendees was invited to partake in a hands-on
   training course where they received touchscreen training covering both
   hardware and software components. Beyond the two touchscreen events,
   virtual platforms have been developed to further support touchscreen
   users: (a) , which includes a data repository of rodent touchscreen
   tasks, and (b) , an online community with numerous training and
   community resources, perhaps most notably a forum where members can ask
   and answer questions. The advantages of the rodent touchscreen
   technology for cognitive neuroscience research has allowed
   neuroscientists from diverse backgrounds to test specific cognitive
   processes using well-validated and standardized apparatus, contributing
   to its rise in popularity and its relevance to modern neuroscience
   research. The commitment of the touchscreen community to data, task
   development and information sharing not only ensures an expansive future
   of the use of rodent touchscreen technology but additionally, quality
   research that will increase translation from preclinical studies to
   clinical successes.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Dumont, JR (Corresponding Author), Univ Western Ontario, Robarts Res Inst, WIRB 6th Floor,Rm 3228,1151 Richmond St N, London, ON N6A 5B7, Canada.
   Dumont, Julie R.; Salewski, Ryan; Beraldo, Flavio, Univ Western Ontario, BrainsCAN, London, ON, Canada.
   Beraldo, Flavio, Univ Western Ontario, Dept Physiol \& Pharmacol, Robarts Res Inst, London, ON, Canada.},
DOI = {10.1111/gbb.12650},
EarlyAccessDate = {APR 2020},
Article-Number = {e12650},
ISSN = {1601-1848},
EISSN = {1601-183X},
Keywords = {Bussey-Saksida; cognitive behavioural testing; mousebytes; ca; open
   science; rodent touch screen; rodent touchscreen; rodent touch-screen;
   touchscreen community; touchscreen resources; touchscreen symposium;
   touchscreencognition; org},
Keywords-Plus = {OPERANT PLATFORM; WORKING-MEMORY; BEHAVIORAL-EVALUATION; CALORIC
   RESTRICTION; COMPUTERIZED TASKS; PERFORMANCE; ATTENTION; MICE; BRAIN;
   TOUCH},
Research-Areas = {Behavioral Sciences; Neurosciences \& Neurology},
Web-of-Science-Categories  = {Behavioral Sciences; Neurosciences},
Author-Email = {jdumont2@uwo.ca},
Affiliations = {Western University (University of Western Ontario); Western University
   (University of Western Ontario)},
ORCID-Numbers = {Dumont, Julie R./0000-0002-2412-306X},
Funding-Acknowledgement = {Canadian First Research Excellence (CFREF) Fund via BrainsCAN;
   International Socitery of Neurochemistry (ISN)},
Funding-Text = {Canadian First Research Excellence (CFREF) Fund via BrainsCAN;
   International Socitery of Neurochemistry (ISN)},
Number-of-Cited-References = {55},
Times-Cited = {23},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Genes Brain Behav.},
Doc-Delivery-Number = {QA4LP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000522772100001},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:001056751200056,
Author = {Sofi-Mahmudi, Ahmad and Raittio, Eero and Uribe, Sergio},
Title = {Transparency of COVID-19-related research: A meta-research study},
Journal = {PLOS ONE},
Year = {2023},
Volume = {18},
Number = {7},
Month = {JUL 26},
Abstract = {BackgroundWe aimed to assess the adherence to five transparency
   practices (data availability, code availability, protocol registration
   and conflicts of interest (COI), and funding disclosures) from open
   access Coronavirus disease 2019 (COVID-19) related articles. MethodsWe
   searched and exported all open access COVID-19-related articles from
   PubMed-indexed journals in the Europe PubMed Central database published
   from January 2020 to June 9, 2022. With a validated and automated tool,
   we detected transparent practices of three paper types: research
   articles, randomized controlled trials (RCTs), and reviews. Basic
   journal- and article-related information were retrieved from the
   database. We used R for the descriptive analyses. ResultsThe total
   number of articles was 258,678, of which we were able to retrieve full
   texts of 186,157 (72\%) articles from the database Over half of the
   papers (55.7\%, n = 103,732) were research articles, 10.9\% (n = 20,229)
   were review articles, and less than one percent (n = 1,202) were RCTs.
   Approximately nine-tenths of articles (in all three paper types) had a
   statement to disclose COI. Funding disclosure (83.9\%, confidence
   interval (CI): 81.7-85.8 95\%) and protocol registration (53.5\%, 95\%
   CI: 50.7-56.3) were more frequent in RCTs than in reviews or research
   articles. Reviews shared data (2.5\%, 95\% CI: 2.3-2.8) and code (0.4\%,
   95\% CI: 0.4-0.5) less frequently than RCTs or research articles.
   Articles published in 2022 had the highest adherence to all five
   transparency practices. Most of the reviews (62\%) and research articles
   (58\%) adhered to two transparency practices, whereas almost half of the
   RCTs (47\%) adhered to three practices. There were journal- and
   publisher-related differences in all five practices, and articles that
   did not adhere to transparency practices were more likely published in
   lowest impact journals and were less likely cited. ConclusionWhile most
   articles were freely available and had a COI disclosure, adherence to
   other transparent practices was far from acceptable. A much stronger
   commitment to open science practices, particularly to protocol
   registration, data and code sharing, is needed from all stakeholders.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Sofi-Mahmudi, A (Corresponding Author), McMaster Univ, Natl Pain Ctr, Dept Anesthesia, Hamilton, ON, Canada.
   Sofi-Mahmudi, A (Corresponding Author), McMaster Univ, Dept Hlth Res Methods Evidence \& Impact, Hamilton, ON, Canada.
   Sofi-Mahmudi, A (Corresponding Author), Kurdistan Univ Med Sci, Seqiz Hlth Network, Seqiz, Kurdistan, Iran.
   Sofi-Mahmudi, Ahmad, McMaster Univ, Natl Pain Ctr, Dept Anesthesia, Hamilton, ON, Canada.
   Sofi-Mahmudi, Ahmad, McMaster Univ, Dept Hlth Res Methods Evidence \& Impact, Hamilton, ON, Canada.
   Sofi-Mahmudi, Ahmad, Kurdistan Univ Med Sci, Seqiz Hlth Network, Seqiz, Kurdistan, Iran.
   Raittio, Eero, Univ Eastern Finland, Inst Dent, Kuopio, Finland.
   Raittio, Eero, Aarhus Univ, Dept Dent \& Oral Hlth, Aarhus, Denmark.
   Uribe, Sergio, Riga Stradins Univ, Dept Conservat Dent \& Oral Hlth, Riga, Latvia.
   Uribe, Sergio, Univ Austral Chile, Sch Dent, Valdivia, Chile.
   Uribe, Sergio, Riga Tech Univ, Balt Biomat Ctr Excellence, Headquarters, Riga, Latvia.},
DOI = {10.1371/journal.pone.0288406},
ISSN = {1932-6203},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {sofima@mcmaster.ca},
Affiliations = {McMaster University; McMaster University; Kurdistan University of
   Medical Sciences; University of Eastern Finland; Aarhus University; Riga
   Stradins University; Universidad Austral de Chile; Riga Technical
   University},
ResearcherID-Numbers = {Raittio, Eero/AAA-8012-2021
   Sofi-Mahmudi, Ahmad/AAO-5069-2021},
ORCID-Numbers = {Raittio, Eero/0000-0002-9258-9355
   Sofi-Mahmudi, Ahmad/0000-0001-6829-0823},
Funding-Acknowledgement = {European Union's Horizon 2020 {[}857287]; Uznemuma MikroTik ligumam
   {[}UL8]; Finnish Dental Society Apollonia; Aarhus University Research
   Foundation {[}AUFF-E 2019-7-3]; Headquarters at Riga Technical
   University, Riga, Latvia},
Funding-Text = {The computational analyses were performed on servers provided by UEF
   Bioinformatics Center, University of Eastern Finland, Finland. Uribe was
   supported by European Union's Horizon 2020 grant 857287 for the Baltic
   Biomaterials Centre of Excellence, Headquarters at Riga Technical
   University, Riga, Latvia and the Uznemuma MikroTik ligumam Nr. UL8, 2021
   RSU (toward implementing the RSU data repository and the FAIR data
   management principles). Raittio was supported by the Finnish Dental
   Society Apollonia and the Aarhus University Research Foundation
   (\#AUFF-E 2019-7-3).},
Number-of-Cited-References = {30},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {Q3SO1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001056751200056},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000811543200001,
Author = {Pinto, Alexander and Cardinale, Yudith and Dongo, Irvin and
   Ticona-Herrera, Regina},
Title = {An Ontology for Modeling Cultural Heritage Knowledge in Urban Tourism},
Journal = {IEEE ACCESS},
Year = {2022},
Volume = {10},
Pages = {61820-61842},
Abstract = {Urban tourism information available on Internet has been of enormous
   relevance to motivate the tourism in many countries. There exist many
   applications focused on promoting and preserving the cultural heritage,
   through urban tourism, which in turn demand a well-defined and standard
   model for representing the whole knowledge of this domain, thus ensuring
   interoperable and flexible applications. Current studies propose the use
   of ontologies to formally model such knowledge. Nonetheless, most of
   them only represent partial knowledge of cultural heritage or are
   restrictive to an indoor perspective (i.e., museum ontologies). In this
   context, we propose the ontology CURIOCITY (Cultural Heritage for Urban
   Tourism in Indoor/Outdoor environments of the CITY), to represent the
   cultural heritage knowledge based on UNESCO's definitions. CURIOCITY
   ontology has a three-level architecture (Upper, Middle, and Lower
   ontologies) in accordance with a purpose of modularity and levels of
   specificity. In this paper, we describe in detail all modules of
   CURIOCITY ontology and perform a comparative evaluation with
   state-of-the-art ontologies. Additionally, to demonstrate the
   suitability of CURIOCITY ontology, we show several touristic services
   offered through a framework supported in the ontology. The framework
   includes an automatic population process, that allows transforming a
   museum data repository (in CSV format) into RDF triples of CURIOCITY
   ontology to automatically populate the CURIOCITY repository, and
   facilities to develop a set of tourism applications and services,
   following the UNESCO's definitions.},
Publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC},
Address = {445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA},
Type = {Article},
Language = {English},
Affiliation = {Cardinale, Y (Corresponding Author), Univ Catolica San Pablo, Elect \& Elect Engn Dept, Arequipa 04001, Peru.
   Cardinale, Y (Corresponding Author), Univ Int Valencia, Escuela Super Ingn Ciencia \& Tecnol, Valencia 46002, Spain.
   Pinto, Alexander; Ticona-Herrera, Regina, Univ Catolica San Pablo, Comp Sci Dept, Arequipa 04001, Peru.
   Cardinale, Yudith; Dongo, Irvin, Univ Catolica San Pablo, Elect \& Elect Engn Dept, Arequipa 04001, Peru.
   Cardinale, Yudith, Univ Int Valencia, Escuela Super Ingn Ciencia \& Tecnol, Valencia 46002, Spain.
   Dongo, Irvin; Ticona-Herrera, Regina, Univ Bordeaux, ESTIA Inst Technol, F-64210 Bidart, France.},
DOI = {10.1109/ACCESS.2022.3179664},
ISSN = {2169-3536},
Keywords = {Ontologies; Cultural differences; Global communication; Urban areas;
   Economics; Sociology; Open data; Automatic population; cultural
   heritage; ontology; ontology evaluation; urban tourism},
Keywords-Plus = {RECOMMENDATION; QUALITY; MUSEUMS; SYSTEM},
Research-Areas = {Computer Science; Engineering; Telecommunications},
Web-of-Science-Categories  = {Computer Science, Information Systems; Engineering, Electrical \&
   Electronic; Telecommunications},
Author-Email = {yudith.cardinale@campusviu.es},
Affiliations = {Universidad Catolica San Pablo; Universidad Catolica San Pablo;
   Universidad Internacional de Valencia VIU; Universite de Bordeaux},
ResearcherID-Numbers = {Dongo, Irvin/W-2118-2018
   },
ORCID-Numbers = {Dongo, Irvin/0000-0003-4859-0428
   Pinto De la Gala, Alexander Giuliano/0000-0002-0807-7606},
Funding-Acknowledgement = {Fondo Nacional de Desarrollo Cientifico, Tecnologico y de Innovacion
   Tecnologica-FONDECYT {[}01-2019-FONDECYT-BM-INC.INV]},
Funding-Text = {This work was supported by the Fondo Nacional de Desarrollo Cientifico,
   Tecnologico y de Innovacion Tecnologica-FONDECYT as an Executing Entity
   of Consejo Nacional de Ciencia, Tecnologia e Innovacion Tecnologica
   (CONCYTEC) through the Project RUTAS: Robots for Urban Tourism,
   Autonomous and Semantic-Based under Grant 01-2019-FONDECYT-BM-INC.INV.},
Number-of-Cited-References = {92},
Times-Cited = {2},
Usage-Count-Last-180-days = {11},
Usage-Count-Since-2013 = {24},
Journal-ISO = {IEEE Access},
Doc-Delivery-Number = {2D4UC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000811543200001},
OA = {gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000600295700005,
Author = {Lim, Cherry and Miliya, Thyl and Chansamouth, Vilada and Aung, Myint
   Thazin and Karkey, Abhilasha and Teparrukkul, Prapit and Rahul, Batra
   and Nguyen Phu Huong Lan and Stelling, John and Turner, Paul and Ashley,
   Elizabeth and van Doorn, H. Rogier and Lin, Htet Naing and Ling, Clare
   and Hinjoy, Soawapak and Iamsirithaworn, Sopon and Dunachie, Susanna and
   Wangrangsimakul, Tri and Hantrakun, Viriya and Schilling, William and
   Lam Minh Yen and Le Van Tan and Htay Htay Hlaing and Mayxay, Mayfong and
   Vongsouvath, Manivanh and Basnyat, Buddha and Edgeworth, Jonathan and
   Peacock, Sharon J. and Thwaites, Guy and Day, Nicholas P. J. and Cooper,
   Ben S. and Limmathurotsakul, Direk},
Title = {Automating the Generation of Antimicrobial Resistance Surveillance
   Reports: Proof-of-Concept Study Involving Seven Hospitals in Seven
   Countries},
Journal = {JOURNAL OF MEDICAL INTERNET RESEARCH},
Year = {2020},
Volume = {22},
Number = {10},
Month = {OCT 2},
Abstract = {Background: Reporting cumulative antimicrobial susceptibility testing
   data on a regular basis is crucial to inform antimicrobial resistance
   (AMR) action plans at local, national, and global levels. However,
   analyzing data and generating a report are time consuming and often
   require trained personnel.
   Objective: This study aimed to develop and test an application that can
   support a local hospital to analyze routinely collected electronic data
   independently and generate AMR surveillance reports rapidly.
   Methods: An offline application to generate standardized AMR
   surveillance reports from routinely available microbiology and hospital
   data files was written in the R programming language (R Project for
   Statistical Computing). The application can be run by double clicking on
   the application file without any further user input. The data analysis
   procedure and report content were developed based on the recommendations
   of the World Health Organization Global Antimicrobial Resistance
   Surveillance System (WHO GLASS). The application was tested on Microsoft
   Windows 10 and 7 using open access example data sets. We then
   independently tested the application in seven hospitals in Cambodia, Lao
   People's Democratic Republic, Myanmar, Nepal, Thailand, the United
   Kingdom, and Vietnam.
   Results: We developed the AutoMated tool for Antimicrobial resistance
   Surveillance System (AMASS), which can support clinical microbiology
   laboratories to analyze their microbiology and hospital data files (in
   CSV or Excel format) onsite and promptly generate AMR surveillance
   reports (in PDF and CSV formats). The data files could be those exported
   from WHONET or other laboratory information systems. The automatically
   generated reports contain only summary data without patient identifiers.
   The AMASS application is downloadable from https://www.amass.website/.
   The participating hospitals tested the application and deposited their
   AMR surveillance reports in an open access data repository.
   Conclusions: The AMASS is a useful tool to support the generation and
   sharing of AMR surveillance reports.},
Publisher = {JMIR PUBLICATIONS, INC},
Address = {130 QUEENS QUAY East, Unit 1100, TORONTO, ON M5A 0P6, CANADA},
Type = {Article},
Language = {English},
Affiliation = {Lim, C (Corresponding Author), Mahidol Univ, Fac Trop Med, Mahidol Oxford Trop Med Res Unit, 3rd Floor,60th Anniversary Chalermprakiat Bldg, Bangkok 10400, Thailand.
   Lim, Cherry; Dunachie, Susanna; Wangrangsimakul, Tri; Hantrakun, Viriya; Schilling, William; Day, Nicholas P. J.; Cooper, Ben S.; Limmathurotsakul, Direk, Mahidol Univ, Fac Trop Med, Mahidol Oxford Trop Med Res Unit, 3rd Floor,60th Anniversary Chalermprakiat Bldg, Bangkok 10400, Thailand.
   Lim, Cherry; Karkey, Abhilasha; Turner, Paul; Ashley, Elizabeth; van Doorn, H. Rogier; Dunachie, Susanna; Wangrangsimakul, Tri; Schilling, William; Mayxay, Mayfong; Basnyat, Buddha; Thwaites, Guy; Day, Nicholas P. J.; Cooper, Ben S.; Limmathurotsakul, Direk, Univ Oxford, Ctr Trop Med \& Global Hlth, Nuffield Dept Med, Oxford, England.
   Miliya, Thyl; Turner, Paul, Angkor Hosp Children, Cambodia Oxford Med Res Unit, Siem Reap, Cambodia.
   Chansamouth, Vilada; Ashley, Elizabeth; Mayxay, Mayfong; Vongsouvath, Manivanh, Lao Oxford Mahosot Hosp Wellcome Trust Res Unit, Mahosot Hosp, Viangchan, Laos.
   Aung, Myint Thazin; Htay Htay Hlaing, North Okkalapa Gen \& Teaching Hosp, Yangon, Myanmar.
   Karkey, Abhilasha; Basnyat, Buddha, Patan Hosp, Kathmandu, Nepal.
   Karkey, Abhilasha; Basnyat, Buddha, Patan Hosp, Oxford Univ Clin Res Unit, Kathmandu, Nepal.
   Teparrukkul, Prapit, Sunpasitthiprasong Hosp, Ubon Ratchathani, Thailand.
   Rahul, Batra; Edgeworth, Jonathan, Kings Coll London, Dept Infect Dis, Ctr Clin Infect \& Diagnost Res, London, England.
   Rahul, Batra; Edgeworth, Jonathan, Guys \& St Thomas NHS Fdn Trust, London, England.
   Nguyen Phu Huong Lan, Hosp Trop Dis, Ho Chi Minh City, Vietnam.
   Stelling, John, Brigham \& Womens Hosp, 75 Francis St, Boston, MA 02115 USA.
   Stelling, John, Harvard Med Sch, Boston, MA 02115 USA.
   Ashley, Elizabeth; Lin, Htet Naing, Myanmar Oxford Clin Res Unit, Yangon, Myanmar.
   van Doorn, H. Rogier; Lam Minh Yen; Le Van Tan; Thwaites, Guy, Univ Oxford, Clin Res Unit, Ho Chi Minh City, Vietnam.
   Ling, Clare, Mahidol Univ, Fac Trop Med, Shoklo Malaria Res Unit, Mae Sot, Thailand.
   Ling, Clare, Mahidol Univ, Fac Trop Med, Mahidol Oxford Trop Med Res Unit, Mae Sot, Thailand.
   Hinjoy, Soawapak, Minist Publ Hlth, Dept Dis Control, Bur Epidemiol, Nonthaburi, Thailand.
   Hinjoy, Soawapak, Minist Publ Hlth, Off Int Cooperat, Dept Dis Control, Nonthaburi, Thailand.
   Iamsirithaworn, Sopon, Minist Publ Hlth, Div Communicable Dis, Dept Dis Control, Nonthaburi, Thailand.
   Mayxay, Mayfong, Univ Hlth Sci, Inst Res \& Educ Dev, Viangchan, Laos.
   Peacock, Sharon J., Univ Cambridge, Dept Med, Cambridge, England.},
DOI = {10.2196/19762},
Article-Number = {e19762},
ISSN = {1438-8871},
Keywords = {antimicrobial resistance; surveillance; report; data analysis;
   application},
Keywords-Plus = {BACTEREMIA},
Research-Areas = {Health Care Sciences \& Services; Medical Informatics},
Web-of-Science-Categories  = {Health Care Sciences \& Services; Medical Informatics},
Author-Email = {cherry@tropmedres.ac},
Affiliations = {Mahidol University; Mahidol Oxford Tropical Medicine Research Unit
   (MORU); University of Oxford; University of London; King's College
   London; Guy's \& St Thomas' NHS Foundation Trust; Harvard University;
   Brigham \& Women's Hospital; Harvard University; Harvard Medical School;
   University of Oxford; Mahidol University; Mahidol University; Mahidol
   Oxford Tropical Medicine Research Unit (MORU); Ministry of Public Health
   - Thailand; Ministry of Public Health - Thailand; Ministry of Public
   Health - Thailand; University of Cambridge},
ResearcherID-Numbers = {van Doorn, H. Rogier/H-3080-2019
   Aung, Myint Thazin/AAZ-9929-2021
   Hinjoy, Soawapak/IYS-6256-2023
   Thwaites, Guy Edward/R-4993-2019
   Cooper, Ben/HGC-7082-2022
   },
ORCID-Numbers = {van Doorn, H. Rogier/0000-0002-9807-1821
   Thwaites, Guy Edward/0000-0002-2858-2087
   Peacock, Sharon/0000-0002-1718-2782
   Lim, Cherry/0000-0003-2555-6980
   Stelling, John/0000-0001-5719-7754
   Ashley, Elizabeth/0000-0002-7620-4822
   Cooper, Ben/0000-0002-9445-7217
   Limmathurotsakul, Direk/0000-0001-7240-5320
   Karkey, Abhilasha/0000-0002-5179-650X
   Schilling, William/0000-0002-6328-8748
   Dunachie, Susanna/0000-0001-5665-6293
   /0000-0002-1075-4135
   Turner, Paul/0000-0002-1013-7815
   Thyl, Miliya/0000-0002-7551-6189},
Funding-Acknowledgement = {Wellcome Trust {[}106698/Z/14/Z, 106680/B/14/Z, 206736]; Intermediate
   Training Fellowship {[}101103]; UK Medical Research Council; Department
   for International Development {[}MR/K006924/1]; MRC {[}MR/K006924/1]
   Funding Source: UKRI},
Funding-Text = {We thank all hospitals that participated in the AMASS project. We thank
   Dr Thet Wai Nwe from the Central Epidemiology Unit of Myanmar and Dr
   Htay Htay Tin from the National Health Laboratory of Myanmar for their
   comments on the AMASS. We also thank Dr Kyi Soe, who is the Senior
   Medical Superintendent of North Okkalapa General and Teaching Hospital,
   for his support for the AMASS and for hosting the AMASS training
   workshop at the hospital. We thank Professor Frank Smithuis and Dr Aung
   Pyae Phyo from Myanmar Oxford Clinical Research Unit (MOCRU) for their
   support on the AMASS project. We thank Professor Paul Newton and
   Professor David Dance from the Lao-Oxford-Mahosot Hospital-Wellcome
   Trust Research Unit (LOMWRU) for their support on the AMASS project. We
   thank Ronas Shakya from Patan Hospital, Nepal for technical assistance.
   We thank Joe Hessell from the Diagnostic Microbiology Development
   Program for comments on the AMASS. We thank Chotipong Chaisiripreeyakul,
   Techat Totemchokchaikarn, Sitthinun Pasirichusaree, and Papitchaya
   Achavakulthep for the tutorial videos on the AMASS. Mahidol Oxford
   Tropical Medicine Research Unit (MORU) is funded by the Wellcome Trust
   (grant: 106698/Z/14/Z). Oxford University Clinical Research Unit (OUCRU)
   is funded by the Wellcome Trust (grant: 106680/B/14/Z). The
   investigators are funded by the Wellcome Trust (CLim is funded by a
   Training Research Fellowship {[}grant: 206736] and DL is funded by an
   Intermediate Training Fellowship {[}grant: 101103]). BC is funded by the
   UK Medical Research Council and Department for International Development
   (grant: MR/K006924/1). The funders of the investigators and study had no
   role in the study, data collection, data analysis, data interpretation,
   or writing of the manuscript. The corresponding authors had the final
   responsibility for the decision to submit for publication.},
Number-of-Cited-References = {38},
Times-Cited = {10},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {6},
Journal-ISO = {J. Med. Internet Res.},
Doc-Delivery-Number = {PH3CQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000600295700005},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001083568600001,
Author = {Balson, Tyler B. and Ward, Adam S.},
Title = {A cloud-based, open-source tool and database for stream solute tracer
   studies},
Journal = {ENVIRONMENTAL MODELLING \& SOFTWARE},
Year = {2023},
Volume = {169},
Month = {NOV},
Abstract = {The growth in cloud-based computing platforms and open data repositories
   is enabling new workflows, standardization of analyses, and synthesis
   projects across many domains, including hydrologic science. Here, we
   established an open-source tool and database for Stream Solute Tracers,
   leveraging community resources including both HydroShare (for data
   storage, curation, and analysis) and HydroLearn (linking our tool to
   disciplinary educational resources). This framework provides users cloud
   access to a toolbox for analysis of experimental data producing an
   standardized analysis for individual experiments. Individual
   experimental results are presented along with fall studies in the
   database, providing context for interpretation of results. Both the
   input and output are aggregated within a PostgreSQL database providing a
   queryable, single database for stream tracer experiments.
   Standardization of the analysis of these experimental results will
   ensure reproducibility for future research, and this is built on a
   discipline-specific platform to reduce barriers to entry for users.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Balson, TB (Corresponding Author), Indiana Univ, Luddy Sch Informat Comp \& Engn, Bloomington, IN 47405 USA.
   Balson, Tyler B., Indiana Univ, Luddy Sch Informat Comp \& Engn, Bloomington, IN 47405 USA.
   Ward, Adam S., Indiana Univ, ONeill Sch Publ \& Environm Affairs, Bloomington, IN USA.
   Ward, Adam S., Oregon State Univ, Biol \& Ecol Engn, Corvallis, OR USA.},
DOI = {10.1016/j.envsoft.2023.105806},
EarlyAccessDate = {SEP 2023},
Article-Number = {105806},
ISSN = {1364-8152},
EISSN = {1873-6726},
Keywords = {Open hydrology; Reproducibility; HydroShare; Jupyter; Data frameworks},
Keywords-Plus = {TRANSIENT STORAGE; MASS-TRANSFER; TRANSPORT; DISCHARGE; WATER;
   EQUATIONS; FRAMEWORK; REGIMES},
Research-Areas = {Computer Science; Engineering; Environmental Sciences \& Ecology; Water
   Resources},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Engineering,
   Environmental; Environmental Sciences; Water Resources},
Author-Email = {tbalson@iu.edu},
Affiliations = {Indiana University System; Indiana University Bloomington; Indiana
   University System; Indiana University Bloomington; Oregon State
   University},
ResearcherID-Numbers = {Ward, Adam/H-7668-2012},
ORCID-Numbers = {Ward, Adam/0000-0002-6376-0061},
Funding-Acknowledgement = {U.S. Department of Energy {[}DE-SC0019377]; National Science Foundation
   {[}EAR-1360276, EAR-1652293]; University of Birmingham (Institute of
   Advanced Studies); Fulbright-University of Birmingham Scholar program;
   CUAHSI Hydroinformatics Innovation Fellowship; Burnell and Barbara
   Fischer Fellowship; U.S. Department of Energy (DOE) {[}DE-SC0019377]
   Funding Source: U.S. Department of Energy (DOE)},
Funding-Text = {This research has been supported by the U.S. Department of Energy
   (DE-SC0019377), the National Science Foundation (grant nos. EAR -1360276
   and EAR-1652293), the 2021 CUAHSI Hydroinformatics Innovation
   Fellowship, the University of Birmingham (Institute of Advanced Studies)
   and the Fulbright-University of Birmingham Scholar program, and with
   resources from the home institutions of the authors including the
   Burnell and Barbara Fischer Fellowship.},
Number-of-Cited-References = {57},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Environ. Modell. Softw.},
Doc-Delivery-Number = {U3AU5},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001083568600001},
DA = {2024-01-15},
}

@article{ WOS:000957522300001,
Author = {Tome, P. and Pesaro, S. and Orioles, M. and Pascotto, E. and Cadamuro,
   A. and Galeotti, M.},
Title = {InfoFaunaFVG: a novel progressive web application for wildlife
   surveillance},
Journal = {EUROPEAN JOURNAL OF WILDLIFE RESEARCH},
Year = {2023},
Volume = {69},
Number = {2},
Month = {APR},
Abstract = {The Department of Agricultural, Food, Environmental and Animal Sciences
   (DI4A) at the University of Udine, in collaboration with Friuli Venezia
   Giulia regional authorities, within northeastern Italy, set up a
   wildlife monitoring and surveillance regional network, named
   InfoFaunaFVG. Here we describe the development and application of this
   data repository system based on a novel progressive web application, and
   report the data gathered in the first two and a half years of its use.
   InfoFaunaFVG is made of a Web Database and an integrated WebGIS system.
   In particular, the following open source softwares are used: Apache HTTP
   Server, Oracle MySQL, Symfony, Apache Tomcat, GeoServer, OpenLayers. The
   web app can be accessed from any web browser or by installing the
   progressive web application in the desktop or mobile devices. In short,
   operating from November 2019, InfoFaunaFVG currently (April 2022)
   contains a total of 40,175 records, from 300 different users, from 16
   institutions. Among all species recorded, mammals were 40\% (16,018) of
   the total, whereas avian species represented 59\% (23,741), and others
   (reptiles and amphibians) 1\% (416), respectively. Two hundred
   twenty-six different species (175 avian and 51 mammals) were recorded.
   Details about causes of death and live animal rescue were reported. To
   date, InfoFaunaFVG has proven to be a successful wildlife data
   repository system providing high quality consistent, accurate and
   traceable data. These had a considerable impact on regional wildlife
   governance. In the authors' knowledge, InfoFaunaFVG is the first example
   described in literature of such a progressive web application,
   coordinated on an institutional level, and not based on
   voluntary-citizen observations. InfoFaunaFVG has the potential to become
   the largest wildlife monitoring and surveillance data repository system
   on a national level.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Orioles, M (Corresponding Author), Univ Udine, Dipartimento Sci Agroalimentari Ambientali \& Anim, DI4A, Udine, Italy.
   Tome, P.; Pesaro, S.; Orioles, M.; Galeotti, M., Univ Udine, Dipartimento Sci Agroalimentari Ambientali \& Anim, DI4A, Udine, Italy.
   Pascotto, E., Azienda ULSS 2 Marca Trevigiana, Dipartimento Prevenz, Treviso, Italy.
   Cadamuro, A., Reg Autonoma Friuli Venezia Giulia, Serv Foreste \& Corpo Forestale, Udine, Italy.},
DOI = {10.1007/s10344-023-01664-4},
Article-Number = {38},
ISSN = {1612-4642},
EISSN = {1439-0574},
Keywords = {Wildlife surveillance; Wildlife management; Progressive web application;
   WebGIS application; Database},
Keywords-Plus = {CITIZEN SCIENCE},
Research-Areas = {Environmental Sciences \& Ecology; Zoology},
Web-of-Science-Categories  = {Ecology; Zoology},
Author-Email = {massimo.orioles@uniud.it},
Affiliations = {University of Udine; ULSS 2 Marca TV; Ospedale Ca' Foncello Treviso},
ResearcherID-Numbers = {Orioles, Massimo/ABO-2310-2022
   },
ORCID-Numbers = {Orioles, Massimo/0000-0002-0344-960X
   tome, paolo/0000-0003-4486-1403},
Funding-Acknowledgement = {Universita degli Studi di Udine within the CRUI-CARE Agreement},
Funding-Text = {Open access funding provided by Universita degli Studi di Udine within
   the CRUI-CARE Agreement.},
Number-of-Cited-References = {29},
Times-Cited = {1},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Eur. J. Wildl. Res.},
Doc-Delivery-Number = {A8JJ1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000957522300001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000772244100001,
Author = {Bhalodiya, Jayendra M. and Keung, Sarah N. Lim Choi and Arvanitis,
   Theodoros N.},
Title = {Magnetic resonance image-based brain tumour segmentation methods: A
   systematic review},
Journal = {DIGITAL HEALTH},
Year = {2022},
Volume = {8},
Month = {MAR},
Abstract = {Background Image segmentation is an essential step in the analysis and
   subsequent characterisation of brain tumours through magnetic resonance
   imaging. In the literature, segmentation methods are empowered by
   open-access magnetic resonance imaging datasets, such as the brain
   tumour segmentation dataset. Moreover, with the increased use of
   artificial intelligence methods in medical imaging, access to larger
   data repositories has become vital in method development. Purpose To
   determine what automated brain tumour segmentation techniques can
   medical imaging specialists and clinicians use to identify tumour
   components, compared to manual segmentation. Methods We conducted a
   systematic review of 572 brain tumour segmentation studies during
   2015-2020. We reviewed segmentation techniques using T1-weighted,
   T2-weighted, gadolinium-enhanced T1-weighted, fluid-attenuated inversion
   recovery, diffusion-weighted and perfusion-weighted magnetic resonance
   imaging sequences. Moreover, we assessed physics or mathematics-based
   methods, deep learning methods, and software-based or semi-automatic
   methods, as applied to magnetic resonance imaging techniques.
   Particularly, we synthesised each method as per the utilised magnetic
   resonance imaging sequences, study population, technical approach (such
   as deep learning) and performance score measures (such as Dice score).
   Statistical tests We compared median Dice score in segmenting the whole
   tumour, tumour core and enhanced tumour. Results We found that
   T1-weighted, gadolinium-enhanced T1-weighted, T2-weighted and
   fluid-attenuated inversion recovery magnetic resonance imaging are used
   the most in various segmentation algorithms. However, there is limited
   use of perfusion-weighted and diffusion-weighted magnetic resonance
   imaging. Moreover, we found that the U-Net deep learning technology is
   cited the most, and has high accuracy (Dice score 0.9) for magnetic
   resonance imaging-based brain tumour segmentation. Conclusion U-Net is a
   promising deep learning technology for magnetic resonance imaging-based
   brain tumour segmentation. The community should be encouraged to
   contribute open-access datasets so training, testing and validation of
   deep learning algorithms can be improved, particularly for diffusion-
   and perfusion-weighted magnetic resonance imaging, where there are
   limited datasets available.},
Publisher = {SAGE PUBLICATIONS LTD},
Address = {1 OLIVERS YARD, 55 CITY ROAD, LONDON EC1Y 1SP, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Bhalodiya, JM (Corresponding Author), Ahmedabad Univ, Sch Engn \& Appl Sci, Commerce Six Rd, Ahmadabad 380009, Gujarat, India.
   Bhalodiya, Jayendra M.; Keung, Sarah N. Lim Choi; Arvanitis, Theodoros N., Univ Warwick, Inst Digital Healthcare, Warwick Mfg Grp, Coventry, W Midlands, England.
   Bhalodiya, Jayendra M., Ahmedabad Univ, Sch Engn \& Appl Sci, Commerce Six Rd, Ahmadabad 380009, Gujarat, India.},
DOI = {10.1177/20552076221074122},
Article-Number = {20552076221074122},
ISSN = {2055-2076},
Keywords = {Brain tumour; magnetic resonance imaging; segmentation; systematic
   review; brain; artificial intelligence},
Keywords-Plus = {GLIOMA; MRI; CLASSIFICATION; TEXTURE; MODEL},
Research-Areas = {Health Care Sciences \& Services; Public, Environmental \& Occupational
   Health; Medical Informatics},
Web-of-Science-Categories  = {Health Care Sciences \& Services; Health Policy \& Services; Public,
   Environmental \& Occupational Health; Medical Informatics},
Author-Email = {jayendra.bhalodiya@warwick.ac.uk},
Affiliations = {University of Warwick; Ahmedabad University},
ResearcherID-Numbers = {Arvanitis, Theodoros N/C-9210-2009
   Lim Choi Keung, Sarah N/HNJ-2930-2023
   },
ORCID-Numbers = {Arvanitis, Theodoros N/0000-0001-5473-135X
   Lim Choi Keung, Sarah N/0000-0001-9608-5990
   Bhalodiya, Jayendra/0000-0001-6540-6835},
Funding-Acknowledgement = {Health Data Research UK {[}HDR-3001]},
Funding-Text = {The authors disclosed receipt of the following financial support for the
   research, authorship, and/or publication of this article: This work was
   supported by the Health Data Research UK (grant number HDR-3001).},
Number-of-Cited-References = {253},
Times-Cited = {3},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {62},
Journal-ISO = {Digit. Health},
Doc-Delivery-Number = {ZX9WV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000772244100001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000419550700003,
Author = {Xu, Xingjian and Hao, Lili and Zhu, Junwei and Zhou, Qing and Song,
   Fuhai and Chen, Tingting and Zhang, Sisi and Dong, Lili and Lan, Li and
   Wang, Yanqing and Liang, Fang and Cao, Jiabao and Liu, Fang and Liu, Lin
   and Wang, Fan and Ma, Yingke and Zhang, Lijuan and Chen, Meili and Tian,
   Dongmei and Li, Cuiping and Du, Zhenglin and Yuan, Na and Zeng, Jingyao
   and Zhang, Zhewen and Wang, Jinyue and Shi, Shuo and Zhang, Yadong and
   Pan, Mengyu and Tang, Bixia and Zou, Dong and Song, Shuhui and Sang,
   Jian and Xia, Lin and Wang, Zhennan and Li, Man and Niu, Guangyi and
   Zhang, Yang and Sheng, Xin and Lu, Mingming and Wang, Qi and Liang, Fang
   and Li, Mengwei and Sun, Shixiang and Li, Rujiao and Yu, Chunlei and
   Wang, Guangyu and Li, Man and Yin, Hongyan and Ma, Lina and Chen,
   Huanxin and Sun, Yubin and Yu, Lei and Zhai, Shuang and Sun, Mingyuan
   and Zhang, Zhang and Zhao, Wenming and Xiao, Jingfa and Bao, Yiming and
   Song, Shuhui and Miao, Ya-Ru and Guo, An-Yuan and Lin, Shaofeng and Xue,
   Yu and Luo, Hao and Gao, Feng and Ma, Wei and Cui, Qinghua and Xu,
   Haodong and BIG Data Ctr and BioCode Team and BioProject BioSample GSA
   Team and GWH Team and GVM Team and GEN Team and MethBank Team and
   Science Wikis Team and Hardware System Administration and Writing Grp
   and AnimalTFDB lncRNASNP Team and dbPAF Team and DEG DoriC Team and
   LncRNADis Team and PLMD Team},
Title = {Database Resources of the BIG Data Center in 2018},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2018},
Volume = {46},
Number = {D1},
Pages = {D14-D20},
Month = {JAN 4},
Abstract = {The BIG Data Center at Beijing Institute of Genomics (BIG) of the
   Chinese Academy of Sciences provides freely open access to a suite of
   database resources in support of worldwide research activities in both
   academia and industry. With the vast amounts of omics data generated at
   ever-greater scales and rates, the BIG Data Center is continually
   expanding, updating and enriching its core database resources through
   big-data integration and value-added curation, including BioCode (a
   repository archiving bioinformatics tool codes), BioProject (a
   biological project library), BioSample (a biological sample library),
   Genome Sequence Archive (GSA, a data repository for archiving raw
   sequence reads), Genome Warehouse (GWH, a centralized resource housing
   genome-scale data), Genome Variation Map (GVM, a public repository of
   genome variations), Gene Expression Nebulas (GEN, a database of gene
   expression profiles based on RNA-Seq data), Methylation Bank (MethBank,
   an integrated databank of DNA methylomes), and Science Wikis (a series
   of biological knowledge wikis for community annotations). In addition,
   three featured web services are provided, viz., BIG Search (search as a
   service; a scalable inter-domain text search engine), BIG SSO (single
   sign-on as a service; a user access control system to gain access to
   multiple independent systems with a single ID and password) and Gsub
   (submission as a service; a unified submission service for all relevant
   resources). All of these resources are publicly accessible through the
   home page of the BIG Data Center at http://bigd.big.ac.cn.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Zhang, Z; Zhao, WM; Xiao, JF; Bao, YM (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Zhang, Z; Xiao, JF; Bao, YM (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Z; Zhao, WM; Xiao, JF; Bao, YM (Corresponding Author), Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Zhang, Z; Zhao, WM; Xiao, JF (Corresponding Author), Fudan Univ, Collaborat Innovat Ctr Genet \& Dev, Shanghai 200438, Peoples R China.
   Xu, Xingjian; Hao, Lili; Zhu, Junwei; Zhou, Qing; Chen, Tingting; Zhang, Sisi; Dong, Lili; Lan, Li; Wang, Yanqing; Liang, Fang; Cao, Jiabao; Liu, Lin; Wang, Fan; Ma, Yingke; Zhang, Lijuan; Chen, Meili; Tian, Dongmei; Li, Cuiping; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Song, Shuhui; Sang, Jian; Xia, Lin; Li, Man; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Liang, Fang; Li, Mengwei; Sun, Shixiang; Li, Rujiao; Yu, Chunlei; Wang, Guangyu; Li, Man; Yin, Hongyan; Ma, Lina; Chen, Huanxin; Sun, Yubin; Yu, Lei; Zhai, Shuang; Sun, Mingyuan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Song, Shuhui, Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Xu, Xingjian; Hao, Lili; Song, Fuhai; Cao, Jiabao; Liu, Lin; Wang, Fan; Ma, Yingke; Zhang, Lijuan; Chen, Meili; Zhang, Zhewen; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Zou, Dong; Sang, Jian; Xia, Lin; Li, Man; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Li, Mengwei; Sun, Shixiang; Yu, Chunlei; Wang, Guangyu; Li, Man; Yin, Hongyan; Ma, Lina; Zhang, Zhang; Xiao, Jingfa; Bao, Yiming, Chinese Acad Sci, Beijing Inst Genom, CAS Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Xu, Xingjian; Zhou, Qing; Song, Fuhai; Cao, Jiabao; Liu, Lin; Wang, Fan; Zhang, Lijuan; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Pan, Mengyu; Tang, Bixia; Sang, Jian; Xia, Lin; Wang, Zhennan; Li, Man; Niu, Guangyi; Zhang, Yang; Sheng, Xin; Lu, Mingming; Wang, Qi; Li, Mengwei; Sun, Shixiang; Yu, Chunlei; Wang, Guangyu; Li, Man; Yin, Hongyan; Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming, Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa, Fudan Univ, Collaborat Innovat Ctr Genet \& Dev, Shanghai 200438, Peoples R China.
   Xu, Xingjian; Liu, Fang, Inner Mongolia Normal Univ, Coll Comp Sci Technol, Hohhot 010010, Inner Mongolia, Peoples R China.
   Wang, Zhennan, Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects, Beijing 100101, Peoples R China.
   Miao, Ya-Ru; Guo, An-Yuan; Lin, Shaofeng; Xue, Yu; Xu, Haodong, Huazhong Univ Sci \& Technol, Coll Life Sci \& Technol, Key Lab Mol Biophys, Minist Educ, Wuhan 430074, Hubei, Peoples R China.
   Miao, Ya-Ru; Guo, An-Yuan; Lin, Shaofeng; Xue, Yu; Xu, Haodong, Huazhong Univ Sci \& Technol, Collaborat Innovat Ctr Biomed Engn, Wuhan 430074, Hubei, Peoples R China.
   Luo, Hao; Gao, Feng, Tianjin Univ, Dept Phys, Tianjin 300072, Peoples R China.
   Luo, Hao; Gao, Feng, Tianjin Univ, Minist Educ, Key Lab Syst Bioengn, Tianjin 300072, Peoples R China.
   Luo, Hao; Gao, Feng, Tianjin Univ, SynBio Res Platform, Collaborat Innovat Ctr Chem Sci \& Engn Tianjin, Tianjin 300072, Peoples R China.
   Ma, Wei; Cui, Qinghua, Peking Univ, Sch Basic Med Sci, MOE Key Lab Cardiovasc Sci, Dept Biomed Informat, Beijing 100191, Peoples R China.
   Ma, Wei, Navy Gen Hosp PLA, Cent Lab, Beijing 100191, Peoples R China.
   Sun, Shixiang, Albert Einstein Coll Med, Dept Genet, Bronx, NY 10461 USA.
   Wang, Guangyu, Baylor Coll Med, Dept Mol \& Cellular Biol, Houston, TX 77030 USA.
   Yin, Hongyan, Hainan Univ, Inst Trop Agr \& Forestry, Hainan Key Lab Sustainable Utilizat Trop Bioresou, Haikou 570228, Hainan, Peoples R China.},
DOI = {10.1093/nar/gkx897},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENE-EXPRESSION; KNOWLEDGE; CURATION; CATALOG; RICE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {zhangzhang@big.ac.cn
   zhangzhang@big.ac.cn
   zhaowm@big.ac.cn
   xiaojingfa@big.ac.cn
   baoym@big.ac.cn},
Affiliations = {Chinese Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese
   Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese Academy
   of Sciences; University of Chinese Academy of Sciences, CAS; Fudan
   University; Inner Mongolia Normal University; Chinese Academy of
   Sciences; Institute of Zoology, CAS; Huazhong University of Science \&
   Technology; Huazhong University of Science \& Technology; Tianjin
   University; Tianjin University; Tianjin University; Peking University;
   Sixth Medical Center of Chinese PLA General Hospital; Yeshiva
   University; Albert Einstein College of Medicine; Baylor College of
   Medicine; Hainan University},
ResearcherID-Numbers = {Ma, Wei/J-6046-2019
   Miao, Ya-Ru/AAW-9047-2021
   Luo, Hao/M-6339-2013
   tian, dongmei/HIR-8892-2022
   Zhang, Zhang/JAX-2097-2023
   Yu, Chunlei/AAI-1802-2021
   song, shuhui/D-6015-2014
   zhang, zheng/HCH-9684-2022
   Sun, Shixiang/GQA-4872-2022
   sun, jiamin/JPY-2155-2023
   Zhang, Qiong/AIC-0940-2022
   Wang, Guangyu/AAM-5940-2021
   wang, yanqing/C-5680-2014
   xiao, jing/HRB-7391-2023
   Xue, Yu/G-5929-2011
   xu, haodong/IAM-9132-2023
   Zhang, Sisi/AFV-4667-2022
   zhang, zhang/GQZ-6804-2022
   li, jiaxin/JNT-5073-2023
   Yin, Hong/AAC-5784-2020
   Gao, Feng/C-9913-2009
   Guo, An-Yuan/K-3656-2012
   Ma, Lina/AAD-2435-2019
   Lin, Shaofeng/GWV-6464-2022
   王, 娅冰/JGE-0541-2023
   Zhang, Lijuan/L-9988-2014
   },
ORCID-Numbers = {Ma, Wei/0000-0003-1044-5612
   Miao, Ya-Ru/0000-0002-1982-3141
   Luo, Hao/0000-0003-2714-8817
   tian, dongmei/0000-0003-0564-625X
   Sun, Shixiang/0000-0001-5499-2963
   Zhang, Qiong/0000-0001-5001-8434
   Wang, Guangyu/0000-0003-4803-7200
   wang, yanqing/0000-0002-3054-3079
   Xue, Yu/0000-0002-9403-6869
   Gao, Feng/0000-0002-9563-3841
   Lin, Shaofeng/0000-0002-1177-5480
   Zhang, Zhang/0000-0001-6603-5060
   Pan, Mengyu/0000-0002-9899-1345
   zhang, si si/0000-0002-3852-4796},
Funding-Acknowledgement = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDB13040500, XDA08020102]; National Key Research Program of China
   {[}2017YFC0907502, 2016YFC0901603, 2017YFC0907503, 2016YFB0201702,
   2016YFC0901903]; National Programs for High Technology Research and
   Development {[}863 Program] {[}2015AA020108, 2015AA020101]; National
   Natural Science Foundation of China {[}31100915, 31200978, 31771465,
   31471248, 31671360, 31571358]; International Partnership Program of the
   Chinese Academy of Sciences {[}153F11KYSB20160008]; Key Program of the
   Chinese Academy of Sciences {[}KJZD-EW-L14]; Key Technology Talent
   Program of the Chinese Academy of Sciences; 100 Talent Program of the
   Chinese Academy of Sciences; Youth Innovation Promotion Association of
   the Chinese Academy of Sciences {[}2017141]; Special Project on
   Precision Medicine under National Key RD Program {[}SQ2017YFSF090210];
   Strategic Priority Research Program of the Chinese Academy of Sciences},
Funding-Text = {Strategic Priority Research Program of the Chinese Academy of Sciences
   {[}XDB13040500 to W.Z. and Z.Z.; XDA08020102 to Z.Z.]; National Key
   Research Program of China {[}2017YFC0907502 to Z.Z.; 2016YFC0901603 to
   W.Z.; 2017YFC0907503, 2016YFB0201702, 2016YFC0901903 to J.X.]; National
   Programs for High Technology Research and Development {[}863 Program;
   2015AA020108 to Z.Z.; 2015AA020101 to F.G.]; National Natural Science
   Foundation of China {[}31100915 to L.H.; 31200978 to L.M.; 31771465 and
   31471248 to J.X.; 31671360 to Y.X.; 31571358 to F.G.]; International
   Partnership Program of the Chinese Academy of Sciences
   {[}153F11KYSB20160008]; Key Program of the Chinese Academy of Sciences
   {[}KJZD-EW-L14 to J.X.]; Key Technology Talent Program of the Chinese
   Academy of Sciences {[}to W.Z.]; The 100 Talent Program of the Chinese
   Academy of Sciences {[}to Y.B. and Z.Z.]; The Youth Innovation Promotion
   Association of the Chinese Academy of Sciences {[}2017141 to S.S.]; The
   Special Project on Precision Medicine under the National Key R\&D
   Program {[}SQ2017YFSF090210 to Y.X.]. Funding for open access charge:
   Strategic Priority Research Program of the Chinese Academy of Sciences.},
Number-of-Cited-References = {30},
Times-Cited = {93},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {67},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {FS1QA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000419550700003},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000942237800003,
Author = {Zhou, Xuan and Xu, Zhihong and Kogut, Ashlynn},
Title = {Research data management needs assessment for social sciences graduate
   students: A mixed methods study},
Journal = {PLOS ONE},
Year = {2023},
Volume = {18},
Number = {2},
Month = {FEB 23},
Abstract = {The complexity and privacy issues inherent in social science research
   data makes research data management (RDM) an essential skill for future
   researchers. Data management training has not fully addressed the needs
   of graduate students in the social sciences. To address this gap, this
   study used a mixed methods design to investigate the RDM awareness,
   preparation, confidence, and challenges of social science graduate
   students. A survey measuring RDM preparedness and training needs was
   completed by 98 graduate students in a school of education at a research
   university in the southern United States. Then, interviews exploring
   data awareness, knowledge of RDM, and challenges related to RDM were
   conducted with 10 randomly selected graduate students. All participants
   had low confidence in using RDM, but United States citizens had higher
   confidence than international graduate students. Most participants were
   not aware of on-campus RDM services, and were not familiar with data
   repositories or data sharing. Training needs identified for social
   science graduate students included support with data documentation and
   organization when collaborating, using naming procedures to track
   versions, data analysis using open access software, and data
   preservation and security. These findings are significant in
   highlighting the topics to cover in RDM training for social science
   graduate students. Additionally, RDM confidence and preparation differ
   between populations so being aware of the backgrounds of students taking
   the training will be essential for designing student-centered
   instruction.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Xu, ZH (Corresponding Author), Texas A\&M Univ, Dept Agr Leadership Educ \& Commun, College Stn, TX 79016 USA.
   Zhou, Xuan, Univ Lib, Texas State Univ, Dept Res Data Serv, San Marcos, TX USA.
   Xu, Zhihong, Texas A\&M Univ, Dept Agr Leadership Educ \& Commun, College Stn, TX 79016 USA.
   Kogut, Ashlynn, Texas A\&M Univ, Dept Teaching Learning \& Culture, College Stn, TX USA.},
DOI = {10.1371/journal.pone.0282152},
ISSN = {1932-6203},
Keywords-Plus = {LIBRARY; PERCEPTIONS; CHEMISTRY; LESSONS},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {xuzhihong@tamu.edu},
Affiliations = {Texas State University System; Texas State University San Marcos; Texas
   A\&M University System; Texas A\&M University College Station; Texas
   A\&M University System; Texas A\&M University College Station},
ORCID-Numbers = {Xu, Zhihong/0000-0002-4769-5597
   Zhou, Xuan/0000-0002-7428-083X
   Kogut, Ashlynn/0000-0001-6281-7567},
Funding-Acknowledgement = {T3: Texas A\&M Triads for Transformation, Texas AM University {[}1762]},
Funding-Text = {This work was supported by T3: Texas A\&M Triads for Transformation
   {[}grant numbers 1762, 2020], Texas A\&M University Institutional
   Funding. The funders had no role in study design, data collection and
   analysis, decision to publish, or preparation of the manuscript. There
   was no additional external funding received for this study.},
Number-of-Cited-References = {48},
Times-Cited = {1},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {20},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {9M4YS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000942237800003},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000673797600001,
Author = {Bose, Priyankar and Roy, Satyaki and Ghosh, Preetam},
Title = {A Comparative NLP-Based Study on the Current Trends and Future
   Directions in COVID-19 Research},
Journal = {IEEE ACCESS},
Year = {2021},
Volume = {9},
Pages = {78341-78355},
Abstract = {COVID-19 is a global health crisis that has altered human life and still
   promises to create ripples of death and destruction in its wake. The sea
   of scientific literature published over a short time-span to understand
   and mitigate this global phenomenon necessitates concerted efforts to
   organize our findings and focus on the unexplored facets of the disease.
   In this work, we applied natural language processing (NLP) based
   approaches on scientific literature published on COVID-19 to infer
   significant keywords that have contributed to our social, economic,
   demographic, psychological, epidemiological, clinical, and medical
   understanding of this pandemic. We identify key terms appearing in COVID
   literature that vary in representation when compared to other
   virus-borne diseases such as MERS, Ebola, and Influenza. We also
   identify countries, topics, and research articles that demonstrate that
   the scientific community is still reacting to the short-term threats
   such as transmissibility, health risks, treatment plans, and public
   policies, underpinning the need for collective international efforts
   towards long-term immunization and drug-related challenges. Furthermore,
   our study highlights several long-term research directions that are
   urgently needed for COVID-19 such as: global collaboration to create
   international open-access data repositories, policymaking to curb future
   outbreaks, psychological repercussions of COVID-19, vaccine development
   for SARS-CoV-2 variants and their long-term efficacy studies, and mental
   health issues in both children and elderly.},
Publisher = {IEEE-INST ELECTRICAL ELECTRONICS ENGINEERS INC},
Address = {445 HOES LANE, PISCATAWAY, NJ 08855-4141 USA},
Type = {Article},
Language = {English},
Affiliation = {Bose, P (Corresponding Author), Virginia Commonwealth Univ, Dept Comp Sci, Med Coll Virginia Campus, Richmond, VA 23284 USA.
   Bose, Priyankar; Ghosh, Preetam, Virginia Commonwealth Univ, Dept Comp Sci, Med Coll Virginia Campus, Richmond, VA 23284 USA.
   Roy, Satyaki, Univ N Carolina, Dept Genet, Chapel Hill, NC 27515 USA.},
DOI = {10.1109/ACCESS.2021.3082108},
ISSN = {2169-3536},
Keywords = {COVID-19; Coronaviruses; Natural language processing; Bibliometrics;
   Analytical models; Data models; Public policy; COVID-19; natural
   language processing; coefficient of variation; mean squared error},
Keywords-Plus = {BIBLIOMETRIC ANALYSIS; SOCIAL MEDIA; EBOLA-VIRUS; CORONAVIRUS;
   INFLUENZA; EPIDEMIOLOGY; INFECTION; VACCINES; OSELTAMIVIR; SARS-COV-2},
Research-Areas = {Computer Science; Engineering; Telecommunications},
Web-of-Science-Categories  = {Computer Science, Information Systems; Engineering, Electrical \&
   Electronic; Telecommunications},
Author-Email = {bosep@vcu.edu},
Affiliations = {Virginia Commonwealth University; University of North Carolina;
   University of North Carolina Chapel Hill},
ResearcherID-Numbers = {Bose, Priyankar/AAL-7284-2021
   },
ORCID-Numbers = {Bose, Priyankar/0000-0002-7943-1422
   Ghosh, Preetam/0000-0003-3880-5886},
Funding-Acknowledgement = {NSF {[}CBET-1802588]},
Funding-Text = {This work was supported by NSF under Grant CBET-1802588.},
Number-of-Cited-References = {123},
Times-Cited = {8},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {32},
Journal-ISO = {IEEE Access},
Doc-Delivery-Number = {TJ9MZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000673797600001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000898606900010,
Author = {Revenko, Artem and Martin-Chozas, Patricia},
Title = {Extraction and Semantic Representation of Domain-Specific Relations in
   Spanish Labour Law},
Journal = {PROCESAMIENTO DEL LENGUAJE NATURAL},
Year = {2022},
Number = {69},
Pages = {105-116},
Month = {SEP},
Abstract = {Despite the freedom of information and the development of various open
   data repositories, the access to legal information to general audience
   remains hindered due to the difficulty of understanding and interpreting
   it. In this paper we aim at employing modern language models to extract
   the most important information from legal documents and structure this
   information in a knowledge graph. This knowledge graph can later be used
   to retrieve information and answer legal question. To evaluate the
   performance of different models we formalize the task as event
   extraction and manually annotate 133 instances. We evaluate two models:
   GRIT and Text2Event. The latter model achieves a better score of
   approximate to 0.8 F-1 score for identifying legal classes and 0.5 F-1
   score for identifying roles in legal relations. We demonstrate how the
   produced legal knowledge graph could be exploited with 2 example use
   cases. Finally, we annotate the whole Workers' Statute using the
   fine-tuned Text2Event model and publish the results in an open
   repository.},
Publisher = {SOC ESPANOLA PROCESAMIENTO LENGUAJE NATURAL-SEPLN},
Address = {DEPT LENGUAJES \& SISTEMAS INFORMATICOS, UNIV ALICANTE, APDO 99,
   ALICANTE, 03080, SPAIN},
Type = {Article},
Language = {English},
Affiliation = {Revenko, A (Corresponding Author), Semant Web Co, Vienna, Austria.
   Revenko, Artem, Semant Web Co, Vienna, Austria.
   Martin-Chozas, Patricia, Univ Politecn Madrid, Ontol Engn Grp, Madrid, Spain.},
DOI = {10.26342/2022-69-9},
ISSN = {1135-5948},
EISSN = {1989-7553},
Keywords = {Information Extraction; Knowledge Graphs; Semantic Web; Legal Domain},
Research-Areas = {Linguistics},
Web-of-Science-Categories  = {Linguistics},
Author-Email = {artem.revenko@semantic-web.com
   patricia.martin@upm.es},
Affiliations = {Universidad Politecnica de Madrid},
Funding-Acknowledgement = {European Union {[}825182]; COST (European Cooperation in Science and
   Technology) {[}(CA18209)16]},
Funding-Text = {This work has been supported by the European Union's Horizon 2020
   research and innovation programme through the Pret-a-LLOD15 project,
   with grant agreement No. 825182, and by COST (European Cooperation in
   Science and Technology) through NexusLinguarum, the ``European network
   for Web-centred linguistic data science{''} COST Action (CA18209)16.},
Number-of-Cited-References = {30},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Proces. Leng. Nat.},
Doc-Delivery-Number = {7A7BN},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000898606900010},
DA = {2024-01-15},
}

@article{ WOS:000318797300006,
Author = {Primiero, Giuseppe},
Title = {Offline and online data: on upgrading functional information to
   knowledge},
Journal = {PHILOSOPHICAL STUDIES},
Year = {2013},
Volume = {164},
Number = {2},
Pages = {371-392},
Month = {JUN},
Abstract = {This paper addresses the problem of upgrading functional information to
   knowledge. Functional information is defined as syntactically
   well-formed, meaningful and collectively opaque data. Its use in the
   formal epistemology of information theories is crucial to solve the
   debate on the veridical nature of information, and it represents the
   companion notion to standard strongly semantic information, defined as
   well-formed, meaningful and true data. The formal framework, on which
   the definitions are based, uses a contextual version of the
   verificationist principle of truth in order to connect functional to
   semantic information, avoiding Gettierization and decoupling from true
   informational contents. The upgrade operation from functional
   information uses the machinery of epistemic modalities in order to add
   data localization and accessibility as its main properties. We show in
   this way the conceptual worthiness of this notion for issues in
   contemporary epistemology debates, such as the explanation of knowledge
   process acquisition from information retrieval systems, and open data
   repositories.},
Publisher = {SPRINGER},
Address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Primiero, G (Corresponding Author), Univ Ghent, Ctr Log \& Philosophy Sci, FWO Res Fdn Flanders, Ghent, Belgium.
   Primiero, Giuseppe, Univ Ghent, Ctr Log \& Philosophy Sci, FWO Res Fdn Flanders, Ghent, Belgium.
   Primiero, Giuseppe, Univ Oxford, IEG, Oxford, England.},
DOI = {10.1007/s11098-012-9860-4},
ISSN = {0031-8116},
EISSN = {1573-0883},
Keywords = {Epistemic modalities; Functional information; Upgrade},
Keywords-Plus = {PHILOSOPHY},
Research-Areas = {Philosophy},
Web-of-Science-Categories  = {Philosophy},
Author-Email = {Giuseppe.Primiero@UGent.be},
Affiliations = {Ghent University; University of Oxford},
ORCID-Numbers = {Primiero, Giuseppe/0000-0003-3264-7100},
Number-of-Cited-References = {45},
Times-Cited = {2},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {13},
Journal-ISO = {Philos. Stud.},
Doc-Delivery-Number = {142KY},
Web-of-Science-Index = {Arts &amp; Humanities Citation Index (A&amp;HCI)},
Unique-ID = {WOS:000318797300006},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000570051900002,
Author = {Goodsell, David S. and Burley, Stephen K.},
Title = {RCSB Protein Data Bank tools for 3D structure-guided cancer research:
   human papillomavirus (HPV) case study},
Journal = {ONCOGENE},
Year = {2020},
Volume = {39},
Number = {43},
Pages = {6623-6632},
Month = {OCT 22},
Abstract = {Atomic-level three-dimensional (3D) structure data for biological
   macromolecules often prove critical to dissecting and understanding the
   precise mechanisms of action of cancer-related proteins and their
   diverse roles in oncogenic transformation, proliferation, and
   metastasis. They are also used extensively to identify potentially
   druggable targets and facilitate discovery and development of both
   small-molecule and biologic drugs that are today benefiting individuals
   diagnosed with cancer around the world. 3D structures of biomolecules
   (including proteins, DNA, RNA, and their complexes with one another,
   drugs, and other small molecules) are freely distributed by the
   open-access Protein Data Bank (PDB). This global data repository is used
   by millions of scientists and educators working in the areas of drug
   discovery, vaccine design, and biomedical and biotechnology research.
   The US Research Collaboratory for Structural Bioinformatics Protein Data
   Bank (RCSB PDB) provides an integrated portal to the PDB archive that
   streamlines access for millions of worldwide PDB data consumers
   worldwide. Herein, we review online resources made available free of
   charge by the RCSB PDB to basic and applied researchers, healthcare
   providers, educators and their students, patients and their families,
   and the curious public. We exemplify the value of understanding
   cancer-related proteins in 3D with a case study focused on human
   papillomavirus.},
Publisher = {SPRINGERNATURE},
Address = {CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Goodsell, DS; Burley, SK (Corresponding Author), Rutgers State Univ, Res Collaboratory Struct Bioinformat Prot Data Ba, Piscataway, NJ 08854 USA.
   Goodsell, DS; Burley, SK (Corresponding Author), Rutgers State Univ, Inst Quantitat Biomed, Piscataway, NJ 08854 USA.
   Goodsell, DS (Corresponding Author), Scripps Res Inst, Dept Integrat Struct \& Computat Biol, La Jolla, CA 92037 USA.
   Burley, SK (Corresponding Author), Rutgers State Univ, Dept Chem \& Chem Biol, Piscataway, NJ 08854 USA.
   Burley, SK (Corresponding Author), Univ Calif San Diego, San Diego Supercomp Ctr, Res Collaboratory Struct Bioinformat Prot Data Ba, La Jolla, CA 92093 USA.
   Burley, SK (Corresponding Author), Univ Calif San Diego, Skaggs Sch Pharm \& Pharmaceut Sci, La Jolla, CA 92093 USA.
   Burley, SK (Corresponding Author), Rutgers State Univ, Rutgers Canc Inst New Jersey, New Brunswick, NJ 08903 USA.
   Goodsell, David S.; Burley, Stephen K., Rutgers State Univ, Res Collaboratory Struct Bioinformat Prot Data Ba, Piscataway, NJ 08854 USA.
   Goodsell, David S.; Burley, Stephen K., Rutgers State Univ, Inst Quantitat Biomed, Piscataway, NJ 08854 USA.
   Goodsell, David S., Scripps Res Inst, Dept Integrat Struct \& Computat Biol, La Jolla, CA 92037 USA.
   Burley, Stephen K., Rutgers State Univ, Dept Chem \& Chem Biol, Piscataway, NJ 08854 USA.
   Burley, Stephen K., Univ Calif San Diego, San Diego Supercomp Ctr, Res Collaboratory Struct Bioinformat Prot Data Ba, La Jolla, CA 92093 USA.
   Burley, Stephen K., Univ Calif San Diego, Skaggs Sch Pharm \& Pharmaceut Sci, La Jolla, CA 92093 USA.
   Burley, Stephen K., Rutgers State Univ, Rutgers Canc Inst New Jersey, New Brunswick, NJ 08903 USA.},
DOI = {10.1038/s41388-020-01461-2},
EarlyAccessDate = {SEP 2020},
ISSN = {0950-9232},
EISSN = {1476-5594},
Keywords-Plus = {CRYSTAL-STRUCTURES; MECHANISM; VALIDATION},
Research-Areas = {Biochemistry \& Molecular Biology; Oncology; Cell Biology; Genetics \&
   Heredity},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology; Oncology; Cell Biology; Genetics \&
   Heredity},
Author-Email = {David.Goodsell@rcsb.org
   Stephen.Burley@rcsb.org},
Affiliations = {Rutgers System; Rutgers New Brunswick; Rutgers System; Rutgers New
   Brunswick; Scripps Research Institute; Rutgers System; Rutgers New
   Brunswick; University of California System; University of California San
   Diego; University of California System; University of California San
   Diego; Rutgers System; Rutgers New Brunswick; Rutgers Biomedical \&
   Health Sciences; Rutgers Cancer Institute of New Jersey},
ORCID-Numbers = {Burley, Stephen K./0000-0002-2487-9713},
Funding-Acknowledgement = {National Science Foundation {[}DBI-1832184]; US Department of Energy
   {[}DE-SC0019749]; National Cancer Institute of the National Institutes
   of Health {[}R01GM133198]; National Institute of General Medical
   Sciences of the National Institutes of Health {[}R01GM133198]; National
   Institute of Allergy and Infectious Diseases of the National Institutes
   of Health {[}R01GM133198]},
Funding-Text = {We gratefully acknowledge discussions with Drs. X.F. Steven Zheng and
   Shridar Ganesan and other members of the Rutgers Cancer Institute of New
   Jersey, and contributions from all members of the RCSB PDB and our wwPDB
   partners around the world. RCSB PDB is jointly funded by grants to SKB
   from the National Science Foundation (DBI-1832184), the US Department of
   Energy (DE-SC0019749), and the National Cancer Institute, National
   Institute of Allergy and Infectious Diseases, and National Institute of
   General Medical Sciences of the National Institutes of Health under
   grant R01GM133198.},
Number-of-Cited-References = {41},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Oncogene},
Doc-Delivery-Number = {OF2UT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000570051900002},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001038409300001,
Author = {Caiado, Helena and Cancela, M. Leonor and Conceicao, Natercia},
Title = {Assessment of MGP gene expression in cancer and contribution to
   prognosis},
Journal = {BIOCHIMIE},
Year = {2023},
Volume = {214},
Number = {B},
Pages = {49-60},
Month = {NOV},
Abstract = {Matrix Gla protein (MGP) was first identified as a calcification
   physiological inhibitor and the causal agent of the Keutel syndrome. MGP
   has been suggested to play a role in development, cell differentiation,
   and tumorigenesis. This study aimed to compare MGP expression and
   methylation status in different tumors and adjacent tissues, using The
   Cancer Genome Atlas (TCGA) data repository. We investigated if changes
   in MGP mRNA expression were correlated to cancer progression and whether
   the correlation coefficients could be used for prognosis. Strong
   correlations were observed between altered MGP levels and disease
   progression in breast, kidney, liver, and thyroid cancers, suggesting
   that it could be used to complement current clinical biomarker assays,
   for early cancer diagnosis. We have also analyzed MGP methylation and
   identified CpG sites in its promoter and first intron with clear
   differences in methylation status between healthy and tumoral tissue
   providing evidence for epigenetic regulation of MGP transcription.
   Furthermore, we demonstrate that these alterations correlate with the
   overall survival of the patients suggesting that its assessment can
   serve as an independent prognostic indicator of patients' survival. \&
   COPY; 2023 The Authors. Published by Elsevier B.V. This is an open
   access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER FRANCE-EDITIONS SCIENTIFIQUES MEDICALES ELSEVIER},
Address = {65 RUE CAMILLE DESMOULINS, CS50083, 92442 ISSY-LES-MOULINEAUX, FRANCE},
Type = {Article},
Language = {English},
Affiliation = {Cancela, ML; Conceiçao, N (Corresponding Author), Univ Algarve, Ctr Marine Sci CCMAR, P-8005139 Faro, Portugal.
   Caiado, Helena, Univ Algarve, ProRegeM PhD Programme Mech Dis \& Regenerat Med, P-8005139 Faro, Portugal.
   Caiado, Helena; Cancela, M. Leonor; Conceicao, Natercia, Univ Algarve, Ctr Marine Sci CCMAR, P-8005139 Faro, Portugal.
   Caiado, Helena; Cancela, M. Leonor; Conceicao, Natercia, Univ Algarve, Fac Med \& Biomed Sci, P-8005139 Faro, Portugal.
   Cancela, M. Leonor; Conceicao, Natercia, Univ Algarve, Algarve Biomed Ctr, P-8005139 Faro, Portugal.},
DOI = {10.1016/j.biochi.2023.06.004},
EarlyAccessDate = {JUN 2023},
ISSN = {0300-9084},
EISSN = {1638-6183},
Keywords = {Matrix gla protein; Epigenetics; Methylation; Gene expression; The
   cancer genome atlas},
Keywords-Plus = {MATRIX GLA-PROTEIN; INHIBITOR},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {lcancela@ualg.pt},
Affiliations = {Universidade do Algarve; Universidade do Algarve; Universidade do
   Algarve; Universidade do Algarve},
ORCID-Numbers = {Conceicao, Natercia/0000-0002-5057-0912},
Funding-Acknowledgement = {Portuguese Science and Technology Foundation (FCT) {[}UIDB/04326/2020,
   UIDP/04326/2020, LA/P/0101/2020]; FCT {[}PD/BD/128341/2017]},
Funding-Text = {This research was supported in part by national funds through the
   Portuguese Science and Technology Foundation (FCT) , under the project
   UIDB/04326/2020, UIDP/04326/2020 and LA/P/0101/2020 (CCMAR) . HC was
   supported by a doctoral fellowship (Grant number: PD/BD/128341/2017)
   from FCT.},
Number-of-Cited-References = {27},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Biochimie},
Doc-Delivery-Number = {N6XE2},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001038409300001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000651581100001,
Author = {Bandeira, Nuno and Deutsch, Eric W. and Kohlbacher, Oliver and Martens,
   Lennart and Vizcaino, Juan Antonio},
Title = {Data Management of Sensitive Human Proteomics Data: Current Practices,
   Recommendations, and Perspectives for the Future},
Journal = {MOLECULAR \& CELLULAR PROTEOMICS},
Year = {2021},
Volume = {20},
Abstract = {Today it is the norm that all relevant proteomics data that support the
   conclusions in scientific publications are made available in public
   proteomics data repositories. However, given the increase in the number
   of clinical proteomics studies, an important emerging topic is the
   management and dissemination of clinical, and thus potentially
   sensitive, human proteomics data. Both in the United States and in the
   European Union, there are legal frameworks protecting the privacy of
   individuals. Implementing privacy standards for publicly released
   research data in genomics and transcriptomics has led to processes to
   control who may access the data, so-called ``controlled access{''} data.
   In parallel with the technological developments in the field, it is
   clear that the privacy risks of sharing proteomics data need to be
   properly assessed and managed. In our view, the proteomics community
   must be proactive in addressing these issues. Yet a careful balance must
   be kept. On the one hand, neglecting to address the potential of
   identifiability in human proteomics data could lead to reputational
   damage of the field, while on the other hand, erecting barriers to open
   access to clinical proteomics data will inevitably reduce reuse of
   proteomics data and could substantially delay critical discoveries in
   biomedical research. In order to balance these apparently conflicting
   requirements for data privacy and efficient use and reuse of research
   efforts through the sharing of clinical proteomics data, development
   efforts will be needed at different levels including bioinformatics
   infrastructure, policymaking, and mechanisms of oversight.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Vizcaíno, JA (Corresponding Author), European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge, England.
   Bandeira, Nuno, Univ Calif San Diego UCSD, Ctr Computat Mass Spectrometry, La Jolla, CA USA.
   Bandeira, Nuno, Univ Calif San Diego UCSD, Dept Comp Sci \& Engn, La Jolla, CA USA.
   Bandeira, Nuno, Univ Calif San Diego UCSD, Skaggs Sch Pharm \& Pharmaceut Sci, La Jolla, CA USA.
   Deutsch, Eric W., Inst Syst Biol, Seattle, WA USA.
   Kohlbacher, Oliver, Univ Tubingen, Inst Bioinformat \& Med Informat, Tubingen, Germany.
   Kohlbacher, Oliver, Univ Tubingen, Quantitat Biol Ctr, Tubingen, Germany.
   Kohlbacher, Oliver, Max Planck Inst Dev Biol, Biomol Interact, Tubingen, Germany.
   Kohlbacher, Oliver, Univ Hosp Tubingen, Inst Translat Bioinformat, Tubingen, Germany.
   Martens, Lennart, VIB, VIB UGent Ctr Med Biotechnol, Ghent, Belgium.
   Martens, Lennart, Univ Ghent, Dept Biomol Med, Ghent, Belgium.
   Vizcaino, Juan Antonio, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge, England.},
DOI = {10.1016/j.mcpro.2021.100071},
Article-Number = {100071},
EISSN = {1535-9484},
Keywords-Plus = {IDENTIFICATION; PEPTIDES; GENOMICS; ARCHIVE; ATLAS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemical Research Methods},
Author-Email = {juan@ebi.ac.uk},
Affiliations = {University of California System; University of California San Diego;
   University of California System; University of California San Diego;
   University of California System; University of California San Diego;
   Institute for Systems Biology (ISB); Eberhard Karls University of
   Tubingen; Eberhard Karls University of Tubingen; Max Planck Society;
   Eberhard Karls University of Tubingen; Eberhard Karls University
   Hospital; Flanders Institute for Biotechnology (VIB); Ghent University;
   Ghent University; Wellcome Trust Sanger Institute; European Molecular
   Biology Laboratory (EMBL)},
ResearcherID-Numbers = {Kohlbacher, Oliver/B-7310-2008
   Vizcaino, Juan Antonio/C-3691-2009
   Deutsch, Eric/AAF-5912-2020
   Martens, Lennart/E-8816-2010},
ORCID-Numbers = {Kohlbacher, Oliver/0000-0003-1739-4598
   Vizcaino, Juan Antonio/0000-0002-3905-4335
   Martens, Lennart/0000-0003-4277-658X},
Funding-Acknowledgement = {H2020 EU project EXCELERATE {[}676559]; H2020 EU grant EPIC-XS
   {[}823839]; Wellcome Trust {[}208391/Z/17/Z]; BBSRC {[}BB/P024599/1];
   Ghent University {[}BOF21/GOA/033]; NIH {[}1R01LM013115, NIH
   P41GM103484, R24GM127667, R01GM087221, U19AG023122]; NSF {[}ABI 1759980,
   DBI-1933311]; BBSRC {[}BB/P024599/1] Funding Source: UKRI},
Funding-Text = {The meeting that took place in Amsterdam (April 2019) was funded by
   funds provided by the H2020 EU project EXCELERATE (grant number 676559).
   A second follow-up meeting took place during the Computational
   Proteomics Seminar in Schloss Dagstuhl (Germany) in August 2019.; The
   authors also want to acknowledge the H2020 EU grant EPIC-XS (grant
   number 823839), Wellcome Trust (208391/Z/17/Z), BBSRC grant
   BB/P024599/1, Ghent University grant BOF21/GOA/033, NIH awards
   1R01LM013115, NIH P41GM103484, R24GM127667, R01GM087221, U19AG023122,
   and NSF awards ABI 1759980, DBI-1933311. We also want to acknowledge
   Rhian Howells (EMBL-EBI) for her help in compiling the conclusions of
   the meeting held in Amsterdam. Additionally, the authors wish to thankDr
   VivianOta-Wang of theNational Cancer Institute, NIH, for helpful
   discussions about policies related to privacy and data sharing.},
Number-of-Cited-References = {41},
Times-Cited = {17},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Mol. Cell. Proteomics},
Doc-Delivery-Number = {SD7VF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000651581100001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000703443000002,
Author = {Li, Qian and Ning, Jiangbo and Yuan, Jianping and Xiao, Ling},
Title = {A depthwise separable dense convolutional network with convolution block
   attention module for COVID-19 diagnosis on CT scans},
Journal = {COMPUTERS IN BIOLOGY AND MEDICINE},
Year = {2021},
Volume = {137},
Month = {OCT},
Abstract = {Coronavirus disease 2019 (COVID-19) has caused more than 3 million
   deaths and infected more than 170 million individuals all over the
   world. Rapid identification of patients with COVID-19 is the key to
   control transmission and prevent depletion of hospitals. Several
   networks have been proposed to assist radiologists in diagnosing
   COVID-19 based on CT scans. However, CTs used in these studies are
   unavailable for other researchers to do deeper extensions due to privacy
   concerns. Furthermore, these networks are too heavy-weighted to satisfy
   the general trend applying on a computationally limited platform. In
   this paper, we aim to solve these two problems. Firstly, we establish an
   available dataset COVID-CTx, which contains 828 CT scans positive for
   COVID-19 across 324 patient cases from three open access data
   repositories. To our knowledge, it has the largest number of publicly
   available COVID-19 positive cases compared to other public datasets.
   Secondly, we propose a lightweighted hybrid neural network: Depthwise
   Separable Dense Convolutional Network with Convolution Block Attention
   Module (AM-SdenseNet). AM-SdenseNet synergistically integrates
   Convolutional Block Attention Module with depthwise separable
   convolutions to learn powerful feature representations while reducing
   the parameters to overcome the overfitting problem. Through experiments,
   we demonstrate the superior performance of our proposed AM-SdenseNet
   compared with several state-of-the-art baselines. The excellent
   performance of AM-SdenseNet can improve the speed and accuracy of
   COVID-19 diagnosis, which is extremely useful to control the spreading
   of infection.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Li, Q (Corresponding Author), Chinese Acad Sci, Res Ctr Ultrason \& Technol, Inst Acoust, Beijing 100190, Peoples R China.
   Li, Qian; Ning, Jiangbo; Yuan, Jianping; Xiao, Ling, Chinese Acad Sci, Res Ctr Ultrason \& Technol, Inst Acoust, Beijing 100190, Peoples R China.
   Li, Qian, Univ Chinese Acad Sci, Beijing 100049, Peoples R China.},
DOI = {10.1016/j.compbiomed.2021.104837},
EarlyAccessDate = {SEP 2021},
Article-Number = {104837},
ISSN = {0010-4825},
EISSN = {1879-0534},
Keywords = {COVID-19 diagnosis; CT scan; Dataset light-weighted; DenseNet;
   Convolution block attention module; Depthwise separable convolution},
Keywords-Plus = {LUNG NODULES; CLASSIFICATION},
Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Computer Science;
   Engineering; Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Biology; Computer Science, Interdisciplinary Applications; Engineering,
   Biomedical; Mathematical \& Computational Biology},
Author-Email = {liqian@mail.ioa.ac.cn
   ningjiangbo@mail.ioa.ac.cn
   yuanjianping@mail.ioa.ac.cn
   xiaoling@mail.ioa.ac.cn},
Affiliations = {Chinese Academy of Sciences; Chinese Academy of Sciences; University of
   Chinese Academy of Sciences, CAS},
ResearcherID-Numbers = {wang, wenjuan/JGD-0428-2023},
ORCID-Numbers = {wang, wenjuan/0000-0002-4220-8817},
Number-of-Cited-References = {55},
Times-Cited = {7},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Comput. Biol. Med.},
Doc-Delivery-Number = {WB2YL},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000703443000002},
OA = {Green Published, Bronze},
DA = {2024-01-15},
}

@article{ WOS:000390918300009,
Author = {Russo, Elise and Sittig, Dean F. and Murphy, Daniel R. and Singh,
   Hardeep},
Title = {Challenges in patient safety improvement research in the era of
   electronic health records},
Journal = {HEALTHCARE-THE JOURNAL OF DELIVERY SCIENCE AND INNOVATION},
Year = {2016},
Volume = {4},
Number = {4},
Pages = {285-290},
Month = {DEC},
Abstract = {Electronic health record (EHR) data repositories contain large volumes
   of aggregated, longitudinal clinical data that could allow patient
   safety researchers to identify important safety issues and conduct
   comprehensive evaluations of health care delivery outcomes. However, few
   health systems have successfully converted this abundance of data into
   useful information or knowledge for safety improvement. In this paper,
   we use a case study involving a project on missed/delayed follow-up of
   test results to discuss real-world challenges in using EHR data for
   patient safety research. We identify three types of challenges that pose
   as barriers to advance patient safety improvement research: 1) gaining
   approval to access/review EHR data; 2) interpreting EHR data; 3) working
   with local IT/EHR personnel. We discuss the complexity of these
   challenges, all of which are unlikely to be unique to this project, and
   outline some key next steps that must be taken to support research that
   uses EHR data to improve safety. We recognize that all organizations
   face competing priorities between clinical operations and research.
   However, to leverage EHRs and their abundant data for patient safety
   improvement research, many current data access and security policies and
   procedures must be rewritten and standardized across health care
   organizations. These efforts are essential to help make EHRs and EHR
   data useful for progress in our journey to safer health care. Published
   by Elsevier Inc. This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0).},
Publisher = {ELSEVIER SCIENCE BV},
Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Singh, H (Corresponding Author), Michael E DeBakey VA Med Ctr, Ctr Innovat Qual Effectiveness \& Safety, Houston, TX USA.
   Russo, Elise; Murphy, Daniel R.; Singh, Hardeep, Michael E DeBakey VA Med Ctr, Ctr Innovat Qual Effectiveness \& Safety, Houston, TX USA.
   Russo, Elise; Murphy, Daniel R.; Singh, Hardeep, Baylor Coll Med, Dept Med, Sect Hlth Serv Res, Houston, TX 77030 USA.
   Sittig, Dean F., Univ Texas Hlth Sci Ctr Houston, Sch Biomed Informat, Houston, TX 77030 USA.
   Sittig, Dean F., UT Mem Hermann Ctr Healthcare Qual \& Safety, Houston, TX USA.},
DOI = {10.1016/j.hjdsi.2016.06.005},
ISSN = {2213-0764},
EISSN = {2213-0772},
Keywords-Plus = {INFORMATION-TECHNOLOGY; ADVERSE EVENTS; MEANINGFUL USE; FOLLOW-UP; CARE;
   SYSTEMS; QUALITY; IMPLEMENTATION; SURVEILLANCE; PERFORMANCE},
Research-Areas = {Health Care Sciences \& Services},
Web-of-Science-Categories  = {Health Care Sciences \& Services; Health Policy \& Services},
Author-Email = {hardeeps@bcm.edu},
Affiliations = {Baylor College of Medicine; Baylor College of Medicine; University of
   Texas System; University of Texas Health Science Center Houston},
ResearcherID-Numbers = {Murphy, Daniel R/G-5017-2013
   Sittig, Dean Forrest/D-2471-2009
   },
ORCID-Numbers = {Murphy, Daniel R/0000-0002-2329-668X
   Sittig, Dean Forrest/0000-0001-5811-8915
   SINGH, HARDEEP/0000-0002-4419-8974},
Funding-Acknowledgement = {VA Health Services Research and Development Service {[}CRE 12-033, USA
   14-274]; VA National Center for Patient Safety; Agency for Health Care
   Research and Quality {[}R01HS022087, R21HS023602, P30 HS024459]; Houston
   VA HSR\&D Center for Innovations in Quality, Effectiveness and Safety
   {[}CIN 13-413]},
Funding-Text = {Dr. Singh is supported by the VA Health Services Research and
   Development Service (CRE 12-033; Presidential Early Career Award for
   Scientists and Engineers USA 14-274), the VA National Center for Patient
   Safety, the Agency for Health Care Research and Quality (R01HS022087 and
   R21HS023602), and the Houston VA HSR\&D Center for Innovations in
   Quality, Effectiveness and Safety (CIN 13-413). Drs. Sittig and Singh
   are supported in part by a grant from the Agency for Health Care
   Research and Quality (P30 HS024459).},
Number-of-Cited-References = {59},
Times-Cited = {15},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {7},
Journal-ISO = {HealthCare},
Doc-Delivery-Number = {EG3BI},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000390918300009},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000479299400006,
Author = {Si, Li and Zeng, Yueliang and Guo, Sicheng and Zhuang, Xiaozhe},
Title = {Investigation and analysis of research support services in academic
   libraries},
Journal = {ELECTRONIC LIBRARY},
Year = {2019},
Volume = {37},
Number = {2},
Pages = {281-301},
Month = {APR 1},
Abstract = {Purpose This paper aims at understanding the current situation of
   research support services offered by academic libraries in world-leading
   universities and providing useful implications and insights for other
   academic libraries. Design/methodology/approach Of the top 100
   universities listed in the QS World University Rankings in 2017, 76
   libraries were selected as samples and a website investigation was
   conducted to explore the research support services. The statistical
   method and visualization software was used to generalize the key
   services, and the text analysis and case analysis were applied to reveal
   the corresponding implementation. Findings Research support service has
   become one of the significant services of academic libraries in the
   context of e-research and data-intensive research. The research support
   services can be generally divided into seven aspects, as follows:
   research data management (62, 81.58 per cent), open access (64, 84.21
   per cent), scholarly publishing (59, 77.63 per cent), research impact
   measurement (32, 42.11 per cent), research guides (47, 61.84 per cent),
   research consultation (59, 77.63 per cent) and research tools
   recommendation (38, 50.00 per cent). Originality/value This paper makes
   a comprehensive investigation of research support services in academic
   libraries of top-ranking universities worldwide. The findings will help
   academic libraries improve research support services; thus, advancing
   the work of researchers and promoting scientific discovery.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Zeng, YL (Corresponding Author), Wuhan Univ, Sch Informat Management, Dept Lib Sci, Wuhan, Hubei, Peoples R China.
   Si, Li, Wuhan Univ, Ctr Studies Informat Resources, Dept Lib Sci, Sch Informat Management, Wuhan, Hubei, Peoples R China.
   Si, Li; Guo, Sicheng, Wuhan Univ, Sch Informat Management, Wuhan, Hubei, Peoples R China.
   Zeng, Yueliang, Wuhan Univ, Sch Informat Management, Dept Lib Sci, Wuhan, Hubei, Peoples R China.
   Zhuang, Xiaozhe, Lib Wuhan Univ Technol, Wuhan, Hubei, Peoples R China.},
DOI = {10.1108/EL-06-2018-0125},
ISSN = {0264-0473},
EISSN = {1758-616X},
Keywords = {Academic libraries; Research support; E-research; Data-intensive
   research},
Keywords-Plus = {OPEN ACCESS; DATA-MANAGEMENT; UNIVERSITY; FUTURE},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {zengyueliang2014@163.com},
Affiliations = {Wuhan University; Wuhan University; Wuhan University; Wuhan University
   of Technology},
Funding-Acknowledgement = {National Natural Science Foundation of P.R. China {[}71573198]},
Funding-Text = {This paper is one of the research outcomes of the project supported by
   The National Natural Science Foundation of P.R. China (Project Name:
   Research on the Formation Mechanism and Service of the Federation of
   Institutional Research Data Repository in Big Data Environment, Project
   No. 71573198).},
Number-of-Cited-References = {40},
Times-Cited = {14},
Usage-Count-Last-180-days = {17},
Usage-Count-Since-2013 = {148},
Journal-ISO = {Electron. Libr.},
Doc-Delivery-Number = {IO3SA},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000479299400006},
DA = {2024-01-15},
}

@article{ WOS:000417147400046,
Author = {Bellgard, Matthew I. and Napier, Kathryn R. and Bittles, Alan H. and
   Szer, Jeffrey and Fletcher, Sue and Zeps, Nikolajs and Hunter, Adam A.
   and Goldblatt, Jack},
Title = {Design of a framework for the deployment of collaborative independent
   rare disease-centric registries: Gaucher disease registry model},
Journal = {BLOOD CELLS MOLECULES AND DISEASES},
Year = {2018},
Volume = {68},
Number = {SI},
Pages = {232-238},
Month = {FEB},
Abstract = {Orphan drug clinical trials often are adversely affected by a lack of
   high quality treatment efficacy data that can be reliably compared
   across large patient cohorts derived from multiple governmental and
   country jurisdictions. It is critical that these patient data be
   captured with limited corporate involvement. For some time, there have
   been calls to develop collaborative, non-proprietary, patient-centric
   registries for post-market surveillance of aspects related to orphan
   drug efficacy. There is an urgent need for the development and
   sustainable deployment of these `independent' registries that can
   capture comprehensive clinical, genetic and therapeutic information on
   patients with rare diseases. We therefore extended an open-source
   registry platform, the Rare Disease Registry Framework (RDRF) to
   establish an Independent Rare Disease Registry (IRDR). We engaged with
   an established rare disease community for Gaucher disease to determine
   system requirements, methods of data capture, consent, and reporting. A
   non-proprietary IRDR model is presented that can serve as autonomous
   data repository, but more importantly ensures that the relevant data can
   be made available to appropriate stakeholders in a secure, timely and
   efficient manner to improve clinical decision-making and the lives of
   those with a rare disease. (C) 2017 The Authors. Published by Elsevier
   Inc. This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Bellgard, MI (Corresponding Author), Murdoch Univ, Ctr Comparat Genom, Bldg 390, Murdoch, WA 6150, Australia.
   Bellgard, Matthew I.; Napier, Kathryn R.; Bittles, Alan H.; Fletcher, Sue; Zeps, Nikolajs; Hunter, Adam A., Murdoch Univ, Ctr Comparat Genom, Bldg 390, Murdoch, WA 6150, Australia.
   Bellgard, Matthew I.; Fletcher, Sue, Western Australian Neurosci Res Inst, Nedlands, WA, Australia.
   Bellgard, Matthew I., Macquarie Univ, Bioplatforms Australia, Convenor Australian Bioinformat Facil, N Ryde, NSW, Australia.
   Bittles, Alan H., Edith Cowan Univ, Sch Med \& Hlth Sci, Joondalup, WA, Australia.
   Szer, Jeffrey, Royal Melbourne Hosp, Clin Haematol \& Bone Marrow Transplant Serv, Parkville, Vic, Australia.
   Goldblatt, Jack, King Edward Mem Hosp, Genet Serv, Subiaco, WA, Australia.
   Goldblatt, Jack, King Edward Mem Hosp, Familial Canc Program Western Australia, Subiaco, WA, Australia.},
DOI = {10.1016/j.bcmd.2017.01.013},
ISSN = {1079-9796},
EISSN = {1096-0961},
Keywords = {Gaucher disease; Independent Rare Disease Registry; Open source;
   Post-market surveillance; Rare Disease Registry Framework; Web-based},
Research-Areas = {Hematology},
Web-of-Science-Categories  = {Hematology},
Author-Email = {mbellgard@ccg.murdoch.edu.au
   knapier@ccg.murdoch.edu.au
   abittles@ccg.murdoch.edu.au
   Jeff.Szer@mh.org.au
   sfletcher@ccg.murdoch.edu.au
   nzeps@ccg.murdoch.edu.au
   ahunter@ccg.murdoch.edu.au
   Jack.Goldblatt@health.wa.gov.au},
Affiliations = {Murdoch University; Macquarie University; Edith Cowan University; Royal
   Melbourne Hospital; King Edward Memorial Hospital; University of Western
   Australia; University of Western Australia; King Edward Memorial
   Hospital},
ResearcherID-Numbers = {Zeps, Nikolajs/AAF-3186-2021
   },
ORCID-Numbers = {Zeps, Nikolajs/0000-0002-6404-6839
   Bellgard, Matthew/0000-0002-6303-9469
   Napier, Kathryn/0000-0003-1202-7238},
Funding-Acknowledgement = {Wellcome Trust {[}REF 104746]; Shire Australia Pty. Ltd.; Australian
   National Health and Medical Research Council {[}APP634485, APP1055319];
   EU {[}HEALTH.2012.2.1.1-1-C]},
Funding-Text = {This work was supported by the Wellcome Trust Pathfinder Award {[}REF
   104746] with financial contribution to this award by Shire Australia
   Pty. Ltd. The authors gratefully acknowledge the combined
   support-in-part funding for this work. This includes Australian National
   Health and Medical Research Council {[}APP634485, APP1055319] and the EU
   FP7 Project {[}HEALTH.2012.2.1.1-1-C]: RD Connect: An integrated
   platform connecting databases, registries, biobanks and clinical
   bioinformatics for rare disease research.},
Number-of-Cited-References = {16},
Times-Cited = {15},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Blood Cells Mol. Dis.},
Doc-Delivery-Number = {FO8OR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000417147400046},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000388945600012,
Author = {Petrusic, Darko and Segedinac, Milan and Konjovic, Zora},
Title = {SEMANTIC MODELLING AND ONTOLOGY INTEGRATION OF THE OPEN GOVERNMENT
   SYSTEMS},
Journal = {TEHNICKI VJESNIK-TECHNICAL GAZETTE},
Year = {2016},
Volume = {23},
Number = {6},
Pages = {1631-1641},
Month = {NOV},
Abstract = {Open Government Ontology proposed in this paper is an extensive ontology
   aimed at modelling a wide range of Open Government services. Semantic
   model of the Open Government opens possibilities for the integration
   with other semantic and information models, and enables semantic
   reasoning and resource discovery. Characteristics of the Open Government
   are transparency, participation and collaboration. Main components of
   the Open Government are Open Architecture, Open Data and Open Standards.
   Organizational structure of the Open Government consists of the internal
   government organizations, associated domains and Open (e) Government
   services. Open Government Ontology can be used as a semantic meta-data
   repository for the (e) Government and Open (e) Government services.
   Using formal methods of reasoning with the proposed ontology we can
   search for information about Open (e) Government services and infer on
   gathered knowledge. Also Open Architecture Ontology can be used as
   Information Architecture framework for the creation of these services as
   was the case regarding Montenegrin Semantic Science Network.},
Publisher = {UNIV OSIJEK, TECH FAC},
Address = {TRG IVANE BRLIC-MAZURANIC 2, SLAVONSKI BROD, HR-35000, CROATIA},
Type = {Article},
Language = {English},
Affiliation = {Petrusic, D (Corresponding Author), Minist Sci, Rimski Trg 46, Podgorica 81000, Montenegro.
   Petrusic, Darko, Minist Sci, Rimski Trg 46, Podgorica 81000, Montenegro.
   Segedinac, Milan; Konjovic, Zora, Univ Novi Sad, Fac Tech Sci, Trg Dositeja Obradovica 6, Novi Sad 21000, Serbia.},
DOI = {10.17559/TV-20150514115428},
ISSN = {1330-3651},
EISSN = {1848-6339},
Keywords = {e-Government; ontology; Open Architecture; Open Government; Semantic Web},
Research-Areas = {Engineering},
Web-of-Science-Categories  = {Engineering, Multidisciplinary},
Author-Email = {darko.petrusic@mna.gov.me
   milansegedinac@uns.ac.rs
   ftn\_zora@uns.ac.rs},
Affiliations = {University of Novi Sad},
Number-of-Cited-References = {32},
Times-Cited = {7},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {40},
Journal-ISO = {Teh. Vjesn.},
Doc-Delivery-Number = {ED6DN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000388945600012},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:001000714300022,
Author = {Daniel Padilla-Pantoja, Fabio and Sanchez, Yeison D. and Alfonso
   Quijano-Nieto, Bernardo and Perdomo, Oscar J. and Gonzalez, Fabio A.},
Title = {Etiology of Macular Edema Defined by Deep Learning in Optical Coherence
   Tomography Scans},
Journal = {TRANSLATIONAL VISION SCIENCE \& TECHNOLOGY},
Year = {2022},
Volume = {11},
Number = {9},
Month = {SEP},
Abstract = {Purpose: To develop an automated method based on deep learning (DL) to
   classify macular edema (ME) fromthe evaluation of optical coherence
   tomography (OCT) scans.
   Methods: A total of 4230 images were obtained from data repositories of
   patients attended in an ophthalmology clinic in Colombia and two free
   open-access databases. They were annotated with four biomarkers (BMs) as
   intraretinal fluid, subretinal fluid, hyperreflective foci/tissue, and
   drusen. Then the scans were labeled as control or ocular disease among
   diabetic macular edema (DME), neovascular age-relatedmacular
   degeneration (nAMD), and retinal vein occlusion (RVO) by two expert
   ophthalmologists. Our method was developed by following four consecutive
   phases: segmentation of BMs, the combination of BMs, feature extraction
   with convolutional neural networks to achieve binary classification for
   each disease, and, finally, multiclass classification of diseases and
   control images.
   Results: The accuracy of our model for nAMD was 97\%, and for DME, RVO,
   and control were 94\%, 93\%, and 93\%, respectively. Area under curve
   valueswere 0.99, 0.98, 0.96, and 0.97, respectively. The mean Cohen's
   kappa coefficient for the multiclass classification task was 0.84.
   Conclusions: The proposed DL model may identify OCT scans as normal and
   ME. In addition, itmay classify its cause among three major exudative
   retinal diseases with high accuracy and reliability.
   Translational Relevance: Our DL approach can optimize the efficiency and
   timeliness of appropriate etiological diagnosis of ME, thus improving
   patient access and clinical decision making. It could be useful in
   places with a shortage of specialists and for readers that evaluate OCT
   scans remotely.},
Publisher = {ASSOC RESEARCH VISION OPHTHALMOLOGY INC},
Address = {12300 TWINBROOK PARKWAY, ROCKVILLE, MD 20852-1606 USA},
Type = {Article},
Language = {English},
Affiliation = {Padilla-Pantoja, FD (Corresponding Author), Univ Nacl Colombia, Dept Ophthalmol, Bogota 111321, Colombia.
   Daniel Padilla-Pantoja, Fabio; Alfonso Quijano-Nieto, Bernardo, Univ Nacl Colombia, Dept Ophthalmol, Fac Med, Bogota, Colombia.
   Sanchez, Yeison D.; Gonzalez, Fabio A., Univ Nacl Colombia, MindLab Res Grp, Bogota, Colombia.
   Perdomo, Oscar J., Univ Rosario, Sch Med \& Hlth Sci, Bogota, Colombia.},
DOI = {10.1167/tvst.11.9.29},
Article-Number = {29},
ISSN = {2164-2591},
Keywords = {artificial intelligence; deep learning; computer vision; macular edema;
   optical coherence tomography},
Keywords-Plus = {CLASSIFICATION; DEGENERATION; SEGMENTATION; DISEASES; IMAGES; CARE},
Research-Areas = {Ophthalmology},
Web-of-Science-Categories  = {Ophthalmology},
Author-Email = {fdpadillap@unal.edu.co},
Affiliations = {Universidad Nacional de Colombia; Universidad Nacional de Colombia;
   Universidad del Rosario},
ResearcherID-Numbers = {Padilla-Pantoja, Fabio Daniel/HTR-1595-2023
   Perdomo Charry, Oscar Julian/G-4454-2011},
ORCID-Numbers = {Padilla-Pantoja, Fabio Daniel/0000-0002-3111-3898
   Perdomo Charry, Oscar Julian/0000-0001-9493-2324},
Number-of-Cited-References = {35},
Times-Cited = {3},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Transl. Vis. Sci. Technol.},
Doc-Delivery-Number = {I1UV8},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001000714300022},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000383706500004,
Author = {McManamay, R. A. and Oigbokie, C. O. and Kao, S. -C. and Bevelhimer, M.
   S.},
Title = {Classification of US Hydropower Dams by their Modes of Operation},
Journal = {RIVER RESEARCH AND APPLICATIONS},
Year = {2016},
Volume = {32},
Number = {7},
Pages = {1450-1468},
Month = {SEP},
Abstract = {A key challenge to understanding ecohydrologic responses to dam
   regulation is the absence of a universally transferable classification
   framework for how dams operate. In the present paper, we develop a
   classification system to organize the modes of operation (MOPs) for US
   hydropower dams and powerplants. To determine the full diversity of
   MOPs, we mined federal documents, open-access data repositories, and
   internet sources. We then used CART classification trees to predict MOPs
   based on physical characteristics, regulation, and project generation.
   Finally, we evaluated how much variation MOPs explained in sub-daily
   discharge patterns for stream gages downstream of hydropower dams. After
   reviewing information for 721 dams and 597 power plants, we developed a
   two-tier hierarchical classification based on (i) the storage and
   control of flows to powerplants, and (ii) the presence of a diversion
   around the natural stream bed. This resulted in nine tier-1 MOPs
   representing a continuum of operations from strictly peaking, to
   reregulating, to run-of-river, and two tier-2 MOPs, representing
   diversion and integral dam-powerhouse configurations. Although MOPs
   differed in physical characteristics and energy production,
   classification trees had low accuracies (62\%), which suggested that
   accurate evaluations of MOPs may require individual attention. MOPs and
   dam storage explained 20\% of the variation in downstream subdaily flow
   characteristics and showed consistent alterations in subdaily flow
   patterns from reference streams. This standardized classification scheme
   is important for future research including estimating reservoir
   operations for large-scale hydrologic models and evaluating project
   economics, environmental impacts, and mitigation. Copyright (c) 2016
   John Wiley \& Sons, Ltd.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {McManamay, RA (Corresponding Author), Oak Ridge Natl Lab, Div Environm Sci, One Bethel Valley Rd,Bldg 1504-19,POB 2008, Oak Ridge, TN 37831 USA.
   McManamay, R. A.; Oigbokie, C. O.; Kao, S. -C.; Bevelhimer, M. S., Oak Ridge Natl Lab, Div Environm Sci, One Bethel Valley Rd,Bldg 1504-19,POB 2008, Oak Ridge, TN 37831 USA.},
DOI = {10.1002/rra.3004},
ISSN = {1535-1459},
EISSN = {1535-1467},
Keywords = {large dams; subdaily hydrology; reservoir operation; dam classification;
   hydrologic model},
Keywords-Plus = {ALTERED FLOW REGIMES; ENVIRONMENTAL FLOWS; RESERVOIR-SYSTEM; RIVER;
   WATER; MANAGEMENT},
Research-Areas = {Environmental Sciences \& Ecology; Water Resources},
Web-of-Science-Categories  = {Environmental Sciences; Water Resources},
Author-Email = {mcmanamayra@ornl.gov},
Affiliations = {United States Department of Energy (DOE); Oak Ridge National Laboratory},
ResearcherID-Numbers = {KAO, SHIH-CHIEH/B-9428-2012},
ORCID-Numbers = {KAO, SHIH-CHIEH/0000-0002-3207-5328},
Funding-Acknowledgement = {Department of Energy through the Instream Flow Project; National
   Hydropower Asset Assessment Program; US Department of Energy
   {[}DE-AC05-00OR22725]},
Funding-Text = {This research was sponsored by the Department of Energy through the
   Instream Flow Project and the National Hydropower Asset Assessment
   Program. The data generated from this study, as well as other
   information on the US hydropower resources, are available through Oak
   Ridge National Laboratory's National Hydropower Asset Assessment Program
   website (nhaap.ornl.gov/). We are grateful to Allen Mitchnick, who
   provided assistance with mining FERC e-library, Constantin Scherelis for
   assistance in reviewing FERC documents, and Mike Schramm for providing
   editorial suggestions on an earlier version of this manuscript. This
   paper has been authored by employees of Oak Ridge National Laboratory,
   managed by UT-Battelle, LLC, under contract DE-AC05-00OR22725 with the
   US Department of Energy. Accordingly, the United States Government
   retains and the publisher, by accepting the article for publication,
   acknowledges that the United States Government retains a non-exclusive,
   paid-up, irrevocable, world-wide license to publish or reproduce the
   published form of this manuscript, or allow others to do so, for United
   States Government's purposes.},
Number-of-Cited-References = {46},
Times-Cited = {44},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {39},
Journal-ISO = {River Res. Appl.},
Doc-Delivery-Number = {DW5SF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000383706500004},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000646582000001,
Author = {Bucklin, Ann and Peijnenburg, Katja T. C. A. and Kosobokova, Ksenia N.
   and O'Brien, Todd D. and Blanco-Bercial, Leocadio and Cornils, Astrid
   and Falkenhaug, Tone and Hopcroft, Russell R. and Hosia, Aino and
   Laakmann, Silke and Li, Chaolun and Martell, Luis and Questel, Jennifer
   M. and Wall-Palmer, Deborah and Wang, Minxiao and Wiebe, Peter H. and
   Weydmann-Zwolicka, Agata},
Title = {Toward a global reference database of COI barcodes for marine
   zooplankton},
Journal = {MARINE BIOLOGY},
Year = {2021},
Volume = {168},
Number = {6},
Month = {JUN},
Abstract = {Characterization of species diversity of zooplankton is key to
   understanding, assessing, and predicting the function and future of
   pelagic ecosystems throughout the global ocean. The marine zooplankton
   assemblage, including only metazoans, is highly diverse and
   taxonomically complex, with an estimated similar to 28,000 species of 41
   major taxonomic groups. This review provides a comprehensive summary of
   DNA sequences for the barcode region of mitochondrial cytochrome oxidase
   I (COI) for identified specimens. The foundation of this summary is the
   MetaZooGene Barcode Atlas and Database (MZGdb), a new open-access data
   and metadata portal that is linked to NCBI GenBank and BOLD data
   repositories. The MZGdb provides enhanced quality control and tools for
   assembling COI reference sequence databases that are specific to
   selected taxonomic groups and/or ocean regions, with associated metadata
   (e.g., collection georeferencing, verification of species
   identification, molecular protocols), and tools for statistical
   analysis, mapping, and visualization. To date, over 150,000 COI
   sequences for similar to 5600 described species of marine metazoan
   plankton (including holo- and meroplankton) are available via the MZGdb
   portal. This review uses the MZGdb as a resource for summaries of COI
   barcode data and metadata for important taxonomic groups of marine
   zooplankton and selected regions, including the North Atlantic, Arctic,
   North Pacific, and Southern Oceans. The MZGdb is designed to provide a
   foundation for analysis of species diversity of marine zooplankton based
   on DNA barcoding and metabarcoding for assessment of marine ecosystems
   and rapid detection of the impacts of climate change.},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Review},
Language = {English},
Affiliation = {Bucklin, A (Corresponding Author), Univ Connecticut, Dept Marine Sci, 1080 Shennecossett Rd, Groton, CT 06340 USA.
   Bucklin, Ann, Univ Connecticut, Dept Marine Sci, 1080 Shennecossett Rd, Groton, CT 06340 USA.
   Peijnenburg, Katja T. C. A.; Wall-Palmer, Deborah, Nat Biodivers Ctr, Plankton Divers \& Evolut, Leiden, Netherlands.
   Peijnenburg, Katja T. C. A., Univ Amsterdam, Inst Biodivers \& Ecosyst Dynam, Amsterdam, Netherlands.
   Kosobokova, Ksenia N., Russian Acad Sci, Inst Oceanol, Moscow, Russia.
   O'Brien, Todd D., Natl Marine Fisheries Serv, NOAA, Silver Spring, MD USA.
   Blanco-Bercial, Leocadio, Bermuda Inst Ocean Sci, St Georges, Bermuda.
   Cornils, Astrid; Laakmann, Silke, Alfred Wegener Inst, Helmholtz Ctr Polar \& Marine Res, Bremerhaven, Germany.
   Falkenhaug, Tone, Inst Marine Res, Flodevigen Res Stn, His, Norway.
   Hopcroft, Russell R.; Questel, Jennifer M., Univ Alaska Fairbanks, Inst Marine Sci, Fairbanks, AK USA.
   Hosia, Aino; Martell, Luis, Univ Museum Bergen, Dept Nat Hist, Bergen, Norway.
   Laakmann, Silke, Carl von Ossietzky Univ Oldenburg, Helmholtz Inst Funct Marine Biodivers, Oldenburg, Germany.
   Li, Chaolun; Wang, Minxiao, Chinese Acad Sci, Inst Oceanol, Beijing, Shandong, Peoples R China.
   Wiebe, Peter H., Woods Hole Oceanog Inst, Biol Dept, Falmouth, MA USA.
   Weydmann-Zwolicka, Agata, Univ Gdansk, Inst Oceanog, Gdynia, Poland.},
DOI = {10.1007/s00227-021-03887-y},
Article-Number = {78},
ISSN = {0025-3162},
EISSN = {1432-1793},
Keywords-Plus = {OXIDASE SUBUNIT-I; 16S RIBOSOMAL-RNA; SPECIES IDENTIFICATION; COMMUNITY
   STRUCTURE; NORTH-SEA; COPEPODA CALANOIDA; ARCTIC-OCEAN; COMPARATIVE
   PHYLOGEOGRAPHY; BIODIVERSITY ASSESSMENT; PHYLOGENETIC ANALYSIS},
Research-Areas = {Marine \& Freshwater Biology},
Web-of-Science-Categories  = {Marine \& Freshwater Biology},
Author-Email = {ann.bucklin@uconn.edu},
Affiliations = {University of Connecticut; Naturalis Biodiversity Center; University of
   Amsterdam; Russian Academy of Sciences; National Oceanic Atmospheric
   Admin (NOAA) - USA; Bermuda Institute of Ocean Sciences; Helmholtz
   Association; Alfred Wegener Institute, Helmholtz Centre for Polar \&
   Marine Research; Institute of Marine Research - Norway; University of
   Alaska System; University of Alaska Fairbanks; University of Bergen;
   Carl von Ossietzky Universitat Oldenburg; Chinese Academy of Sciences;
   Institute of Oceanology, CAS; Woods Hole Oceanographic Institution;
   Fahrenheit Universities; University of Gdansk},
ResearcherID-Numbers = {Weydmann-Zwolicka, Agata/AAA-6809-2019
   Li, Chao/GSM-8117-2022
   Kosobokova, Ksenia/P-3363-2014
   Questel, Jennifer/HKW-8698-2023
   Cornils, Astrid/P-2943-2014
   Blanco-Bercial, Leocadio/G-5441-2013
   },
ORCID-Numbers = {Weydmann-Zwolicka, Agata/0000-0002-6655-6613
   Li, Chao/0000-0001-6110-6210
   Kosobokova, Ksenia/0000-0002-3039-4480
   Cornils, Astrid/0000-0003-4536-9015
   Blanco-Bercial, Leocadio/0000-0003-0658-7183
   Bucklin, Ann/0000-0003-3750-9348
   Hosia, Aino/0000-0001-7664-6498
   Li, Chaolun/0000-0003-1890-0587
   Martell, Luis/0000-0002-7062-8915
   Laakmann, Silke/0000-0003-3273-7907
   Wiebe, Peter/0000-0002-6059-4651},
Funding-Acknowledgement = {Scientific Committee on Oceanic Research (SCOR); U.S. National Science
   Foundation {[}OCE-1840868]; Netherlands Organization for Scientific
   Research (NWO) {[}016.161.351]; European Union {[}746186]; Russian
   Foundation for Basic Research {[}18-05-60158, 19-04-00955]; National
   Science Centre, Poland {[}2017/27/B/NZ8/01056]; Fulbright Senior Award;
   Norwegian Taxonomy Initiative of the Norwegian Biodiversity Information
   Centre {[}70184233/HYPNO, 70184240/NORHYDRO, 70184233/COPCLAD,
   70184241/HYPCOP]; Census of Marine Life; NOAA Ocean Exploration and
   Research {[}NA05OAR4601079, NA15OAR0110209]; Ministry for Science and
   Culture of Lower Saxony; Volkswagen Foundation through the
   Niedersachsisches Vorab' grant program {[}ZN3285]; Marie Curie Actions
   (MSCA) {[}746186] Funding Source: Marie Curie Actions (MSCA)},
Funding-Text = {Funding sources for authors of the review paper are described here:
   Scientific Committee on Oceanic Research (SCOR), and a grant to SCOR
   from the U.S. National Science Foundation (OCE-1840868). Netherlands
   Organization for Scientific Research (NWO) Vidi Grant/Award Number:
   016.161.351 to K.T.C.A.P. European Union Horizon 2020 research and
   innovation program under the Marie SklodowskaCurie grant agreement No.
   746186 (POSEIDoN) to D.W.P. The work of K. N.K. was performed in the
   framework of the state assignment of IO RAS (Theme No. 0128-2021-0007)
   and partially supported by Russian Foundation for Basic Research grants
   No. 18-05-60158 and No. 19-04-00955. The work of A.W.Z. was supported by
   a grant from HIDEA-Hidden diversity of the Arctic Ocean (No.
   2017/27/B/NZ8/01056) from the National Science Centre, Poland, and a
   Fulbright Senior Award. The Norwegian Taxonomy Initiative of the
   Norwegian Biodiversity Information Centre provided funding for A.H. and
   L. M. (Project Nos. 70184233/HYPNO and 70184240/NORHYDRO), and for T.F.
   (Project Nos. 70184233/COPCLAD and 70184241/HYPCOP). The work of R.R.H.
   and J.M.Q. was supported by Census of Marine Life and NOAA Ocean
   Exploration and Research (NA05OAR4601079 and NA15OAR0110209). The work
   of S.L. was conducted at the Helmholtz Institute for Functional Marine
   Biodiversity at the University of Oldenburg (HIFMB). HIFMB is a
   collaboration between the AlfredWegener-Institute, Helmholtz-Center for
   Polar and Marine Research, and the Carl-von-Ossietzky University
   Oldenburg, initially funded by the Ministry for Science and Culture of
   Lower Saxony and the Volkswagen Foundation through the Niedersachsisches
   Vorab' grant program (Grant No. ZN3285).},
Number-of-Cited-References = {230},
Times-Cited = {44},
Usage-Count-Last-180-days = {10},
Usage-Count-Since-2013 = {58},
Journal-ISO = {Mar. Biol.},
Doc-Delivery-Number = {RW5SF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000646582000001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000589836300069,
Author = {Kim, Yun Jin and Qian, Linchao and Aslam, Muhammad Shahzad},
Title = {The impact of substance use disorder on the mental health among COVID-19
   patients A protocol for systematic review and meta-analysis},
Journal = {MEDICINE},
Year = {2020},
Volume = {99},
Number = {46},
Month = {NOV 13},
Abstract = {Substance use disorder (SUD) is associated with a high risk of physical
   and mental illness such as anxiety, depression, personality disorders,
   eating disorders, and abnormal mood changes. During the pandemic, SUD, a
   significant problem related to Coronavirus disease 2019 (COVID-19), is
   affecting adolescents. The recent available literature also emphasizes
   understanding the relationship between mental illness and SUD. Hence, it
   is essential to evaluate the scientific approach and examine the
   presented findings of articles published on SUD during the COVID-19
   pandemic. A systematic review will be conducted using PubMed, PubMed
   Central, and Scopus bibliographic databases. The grey literature on the
   impact of SUD on mental health during the COVID-19 pandemic among
   adolescents will be identified using scholar google. The dependability
   and credibility of the findings will be examined using the ConQual
   approach. The methodologies of the included studies will be compared
   using ROBIS (risk of bias in systematic reviews tool), a measurement
   tool to assess systematic reviews (AMSTAR), and the JBI critical
   appraisal tool. The systematic review will be carried out on published
   articles, so it is exempt from ethics approval. The Center for Open
   Science (OSF) will be used as a data repository during the preparation
   of the protocol and completion of the systematic review. The research
   findings will be published in a related peer-reviewed journal.},
Publisher = {LIPPINCOTT WILLIAMS \& WILKINS},
Address = {TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA, PA 19103 USA},
Type = {Review},
Language = {English},
Affiliation = {Aslam, MS (Corresponding Author), Xiamen Univ Malaysia, Sch Tradit Chinese Med, Jalan Sunsuria, Sepang 43900, Selangor, Malaysia.
   Kim, Yun Jin; Qian, Linchao; Aslam, Muhammad Shahzad, Xiamen Univ Malaysia, Sch Tradit Chinese Med, Jalan Sunsuria, Sepang 43900, Selangor, Malaysia.},
DOI = {10.1097/MD.0000000000023203},
Article-Number = {e23203},
ISSN = {0025-7974},
EISSN = {1536-5964},
Keywords = {adolescents; COVID-19; mental health; substance use disorder},
Keywords-Plus = {PREVALENCE; TOOL},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {aslam.shahzad@xmu.edu.my},
Affiliations = {Xiamen University Malaysia Campus},
ResearcherID-Numbers = {Aslam, Muhammad Shahzad/Q-1026-2015
   Kim, Yun Jin/AAE-8281-2019},
ORCID-Numbers = {Aslam, Muhammad Shahzad/0000-0003-2728-6726
   },
Funding-Acknowledgement = {Research Management Centre, Xiamen University Malaysia {[}XMUMRF/2020 -
   C6/ITCM/0004]},
Funding-Text = {This work is supported by the Research Management Centre, Xiamen
   University Malaysia, grants number XMUMRF/2020 - C6/ITCM/0004. The
   funding body had no role in the design and conduct of this study;
   collection, management, analysis, and interpretation of the data;
   preparation, review, or approval of the manuscript; or the decision to
   submit the manuscript for publication.},
Number-of-Cited-References = {32},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Medicine (Baltimore)},
Doc-Delivery-Number = {OS0ED},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000589836300069},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000417613500004,
Author = {Sayed, Awny and Al Muqrishi, Amal},
Title = {IBRI-CASONTO: Ontology-based semantic search engine},
Journal = {EGYPTIAN INFORMATICS JOURNAL},
Year = {2017},
Volume = {18},
Number = {3},
Pages = {181-192},
Month = {NOV},
Abstract = {The vast availability of information, that added in a very fast pace, in
   the data repositories creates a challenge in extracting correct and
   accurate information. Which has increased the competition among
   developers in order to gain access to technology that seeks to
   understand the intent researcher and contextual meaning of terms. While
   the competition for developing an Arabic Semantic Search systems are
   still in their infancy, and the reason could be traced back to the
   complexity of Arabic Language. It has a complex morphological,
   grammatical and semantic aspects, as it is a highly inflectional and
   derivational language. In this paper, we try to highlight and present an
   Ontological Search Engine called IBRI-CASONTO for Colleges of Applied
   Sciences, Oman. Our proposed engine supports both Arabic and English
   language. It is also employed two types of search which are a
   keyword-based search and a semantics-based search. IBRI-CASONTO is based
   on different technologies such as Resource Description Framework (RDF)
   data and Ontological graph. The experiments represent in two sections,
   first it shows a comparison among Entity-Search and the Classical-Search
   inside the IBRI-CASONTO itself, second it compares the EntitySearch of
   IBRI-CASONTO with currently used search engines, such as Kngine, Wolfram
   Alpha and the most popular engine nowadays Google, in order to measure
   their performance and efficiency. (C) 2017 Production and hosting by
   Elsevier B.V. on behalf of Faculty of Computers and Information, Cairo
   University. This is an open access article under the CC BY-NC-ND
   license.},
Publisher = {CAIRO UNIV, FAC COMPUTERS \& INFORMATION},
Address = {AHMED ZEWAIL, AD DOQI, GIZA GOVERNORATE, 00000, EGYPT},
Type = {Article},
Language = {English},
Affiliation = {Sayed, A (Corresponding Author), Menia Univ, Fac Sci, Al Minya, Egypt.
   Sayed, Awny, Menia Univ, Fac Sci, Al Minya, Egypt.
   Al Muqrishi, Amal, Nizwa Univ, Birkat Al Mawz, Oman.},
DOI = {10.1016/j.eij.2017.01.001},
ISSN = {1110-8665},
EISSN = {2090-4754},
Keywords = {Ontological search engine; Keyword-based search; Semantics-based search;
   Resource Description Framework (RDF); Ontological graph},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Artificial Intelligence; Computer Science, Information
   Systems; Computer Science, Software Engineering},
Author-Email = {awny.sayed@mu.edu.eg
   amalsyedsultan@gmail.com},
Affiliations = {Egyptian Knowledge Bank (EKB); Minia University; University of Nizwa},
ResearcherID-Numbers = {Sayed, Awny/AAW-4901-2021},
Number-of-Cited-References = {21},
Times-Cited = {15},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Egypt. Inform. J.},
Doc-Delivery-Number = {FP4UX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000417613500004},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:001114691300022,
Author = {Paton, Norman W. and Chen, Jiaoyan and Wu, Zhenyu},
Title = {Dataset Discovery and Exploration: A Survey},
Journal = {ACM COMPUTING SURVEYS},
Year = {2024},
Volume = {56},
Number = {4},
Month = {APR},
Abstract = {Data scientists are tasked with obtaining insights from data. However,
   suitable data is often not immediately at hand, and there may be many
   potentially relevant datasets in a data lake or in open data
   repositories. As a result, data discovery and exploration are necessary,
   but often time consuming, steps in a data analysis workflow. Data
   discovery is the process of identifying datasets that may meet an
   information need. Data exploration is the process of understanding the
   properties of candidate datasets and the relationships between them.
   Data discovery and data exploration often go hand in hand and benefit
   from tool support. This article surveys research areas that can
   contribute to data discovery and exploration, particularly considering
   dataset search, data navigation, data annotation and schema inference.
   For each of these areas, we identify key dimensions that can be used to
   characterize approaches and the values they can hold, and apply the
   dimensions to describe and compare prominent results. In addition, by
   surveying several adjacent areas that are often considered in isolation,
   we identify recurring techniques and alternative approaches to related
   challenges, thereby placing results within a wider context than is
   generally considered.},
Publisher = {ASSOC COMPUTING MACHINERY},
Address = {1601 Broadway, 10th Floor, NEW YORK, NY USA},
Type = {Article},
Language = {English},
Affiliation = {Paton, NW (Corresponding Author), Univ Manchester, Dept Comp Sci, Oxford Rd, Manchester M13 9PL, Lancs, England.
   Paton, Norman W.; Chen, Jiaoyan; Wu, Zhenyu, Univ Manchester, Dept Comp Sci, Oxford Rd, Manchester M13 9PL, Lancs, England.},
DOI = {10.1145/3626521},
Article-Number = {102},
ISSN = {0360-0300},
EISSN = {1557-7341},
Keywords = {Data search; data navigation; data annotation; data lake; schema
   inference},
Keywords-Plus = {TABLES; SEARCH; SCALE},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Theory \& Methods},
Author-Email = {norman.paton@manchester.ac.uk
   jiaoyan.chen@manchester.ac.uk
   zhenyu.wu@postgrad.manchester.ac.uk},
Affiliations = {University of Manchester},
Number-of-Cited-References = {107},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {ACM Comput. Surv.},
Doc-Delivery-Number = {Z8RL0},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001114691300022},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:001029916600001,
Author = {Cheema, Sehrish Munawar and Tariq, Saman and Pires, Ivan Miguel},
Title = {A natural language interface for automatic generation of data flow
   diagram using web extraction techniques},
Journal = {JOURNAL OF KING SAUD UNIVERSITY-COMPUTER AND INFORMATION SCIENCES},
Year = {2023},
Volume = {35},
Number = {2},
Pages = {626-640},
Month = {FEB},
Abstract = {To model the data and functions in various computer science
   applications, the researcher uses a Data Flow Diagram (DFD). DFD has
   been constructed using {[}open-source software tools that provide users
   with different shapes and environments. However, the existing approaches
   require substantial human effort, the validity of the generated output
   is still a loophole, and they have never gained traction in practice.
   Our research objective is to develop a semi-automated tool for drawing
   complex Data Flow Diagrams in the shortest time according to the
   specified features of the intended system. We developed a Natural
   Language Interface (NLI) that allows the user to compose a query and
   identify the system functionality and constraints for the composition of
   DFD. Natural Language Processing (NLP) techniques are applied to
   scrapped data to extract the keywords and develop a data repository.
   Also, we developed rule-based algorithms to map user queries onto
   respective token shapes to draw the required functionality into
   appropriate levels of DFD. For verification, output DFDs were converted
   into conceptual digraphs using adjacency and permutation matrices to
   evaluate isomorphism. The empirical results reflect that the DFDs
   generated by the system are correct, complete, and significant.\& COPY;
   2023 The Author(s). Published by Elsevier B.V. on behalf of King Saud
   University. This is an open access article under the CC BY-NC-ND license
   (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Tariq, S (Corresponding Author), Univ Management \& Technol, Dept Comp Sci, Sialkot, Pakistan.
   Pires, IM (Corresponding Author), Univ Beira Interior, Inst Telecomunicacoes, Covilha, Portugal.
   Cheema, Sehrish Munawar; Tariq, Saman, Univ Management \& Technol, Dept Comp Sci, Sialkot, Pakistan.
   Pires, Ivan Miguel, Univ Beira Interior, Inst Telecomunicacoes, Covilha, Portugal.},
DOI = {10.1016/j.jksuci.2023.01.006},
EarlyAccessDate = {MAR 2023},
ISSN = {1319-1578},
EISSN = {2213-1248},
Keywords = {Data flow; Business logic; Decomposition; Data flow visualisation
   systems; NLP; Natural Language Interface (NLI); Web scraping; Crawler;
   Graph theory; Adjacency matrices},
Keywords-Plus = {INFORMATION; TIQI},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Information Systems},
Author-Email = {samantariq786@gmail.com
   impires@it.ubi.pt},
Affiliations = {University of Management \& Technology (UMT); Universidade da Beira
   Interior},
ResearcherID-Numbers = {Tariq, Saman/JND-7650-2023
   Pires, Ivan Miguel/V-3573-2017
   },
ORCID-Numbers = {Pires, Ivan Miguel/0000-0002-3394-6762
   tariq, saman/0000-0001-7516-4008
   Munawar, Sehrish/0000-0001-7382-181X},
Funding-Acknowledgement = {FCT/MEC through national funds; FEDER-PT2020 {[}UIDB/50008/2020]; COST
   Action {[}CA16226]; COST (European Cooperation in Science and
   Technology)},
Funding-Text = {This work is funded by FCT/MEC through national funds and co-funded by
   FEDER-PT2020 partnership agreement under the project UIDB/50008/2020.
   This article is based upon work from COST Action
   IC1303-AAPELE-Architectures, Algorithms and Protocols for Enhanced
   Living Environments and COST Action CA16226-SH ELD-ON-Indoor living
   space improvement: Smart Habitat for the Elderly, supported by COST
   (European Cooperation in Science and Technology) . More information is
   available at www.cost.eu.},
Number-of-Cited-References = {83},
Times-Cited = {1},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. King Saud Univ.-Comput. Inf. Sci.},
Doc-Delivery-Number = {M4KS7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001029916600001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000792768300005,
Author = {Alrefaei, Abdulwahed Fahad and Albeshr, Mohammed Fahad and Pizzio,
   Gaston A.},
Title = {16S rRNA gene identification and phylogenetic analysis of dhofar toad
   (Bufo dhufarensis) from riyadh province, saudi arabia},
Journal = {JOURNAL OF KING SAUD UNIVERSITY SCIENCE},
Year = {2022},
Volume = {34},
Number = {4},
Month = {JUN},
Abstract = {The Arabian Peninsula is home to many unique organisms due to its
   distinctive geographical location. Seven species of amphibians inhabit
   Saudi Arabia. One of them is the Dhofar toad (Bufo dhufarensis), a
   species of toad in the family Bufonidae found in Saudi Arabia, the
   United Arab Emirates, Yemen and Oman. This species lives near freshwater
   springs, pools, dams, rivers and rural gardens. By evaluating the
   genetic variety within evolutionary lineages using sequence analysis, we
   were able to determine the degree of genetic diversity of the Dhofar
   toad (Bufo dhufarensis). Additionally, we examine the prob-able
   connections between this species and other toads and frogs. We collected
   27 samples from Bufo dhu-farensis and prepared the samples for DNA
   extraction and PCR using suitable primers. The 16S ribosomal RNA (rRNA)
   gene sequences in toads from Riyadh Province were determined for the
   first time and depos-ited in a public gene data repository. Bufo
   dhufarensis, which was found in Riyadh Province, is very clo-sely
   related to the toad Bufo dhufarensis, which was found in Oman, according
   to a phylogenetic tree based on the 16S rRNA sequence. This is the first
   report of the genetic diversity of Bufo dhufarensis in Riyadh Province
   based on the 16S rRNA gene.(c) 2022 The Author(s). Published by Elsevier
   B.V. on behalf of King Saud University. This is an open access article
   under the CC BY license (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Alrefaei, AF (Corresponding Author), King Saud Univ, Coll Sci, Dept Zool, POB 2455, Riyadh 11451, Saudi Arabia.
   Alrefaei, Abdulwahed Fahad; Albeshr, Mohammed Fahad, King Saud Univ, Coll Sci, Dept Zool, POB 2455, Riyadh 11451, Saudi Arabia.
   Pizzio, Gaston A., Univ Politecn Valencia, Inst Biol Mol \& Celular Plantas, CSIC, ES-46022 Valencia, Spain.},
DOI = {10.1016/j.jksus.2022.101972},
EarlyAccessDate = {MAR 2022},
Article-Number = {101972},
ISSN = {1018-3647},
EISSN = {2213-686X},
Keywords = {Bufo dhufarensis; 16S ribosomal RNA; Phylogenetic tree; Genetic
   distance; Molecular analysis},
Keywords-Plus = {ANURA; EVOLUTIONARY},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {afrefaei@ksu.edu.sa},
Affiliations = {King Saud University; Consejo Superior de Investigaciones Cientificas
   (CSIC); Universitat Politecnica de Valencia; CSIC-UPV - Instituto de
   Biologia Molecular y Celular de Plantas (IBMCP)},
ResearcherID-Numbers = {Alrefaei, Abdulwahed Fahad/AAX-7443-2021
   Pizzio, Gaston/P-9697-2015},
ORCID-Numbers = {Alrefaei, Abdulwahed Fahad/0000-0002-3761-6656
   Pizzio, Gaston/0000-0002-4336-6470},
Funding-Acknowledgement = {King Saud University, Riyadh, Saudi Arabia {[}RSP-2021/218]},
Funding-Text = {Acknowledgements We extend our appreciation to the Researchers
   Supporting Pro-ject number (RSP-2021/218) , King Saud University,
   Riyadh, Saudi Arabia.},
Number-of-Cited-References = {32},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. King Saud Univ. Sci.},
Doc-Delivery-Number = {1B9RT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000792768300005},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000451467500001,
Author = {Scott, Terence P. and Coetzer, Andre and Fahrion, Anna S. and Nel, Louis
   H.},
Title = {Addressing the Disconnect between the estimated, reported, and true
   rabies Data: the Development of a regional African rabies Bulletin},
Journal = {FRONTIERS IN VETERINARY SCIENCE},
Year = {2017},
Volume = {4},
Month = {FEB 20},
Abstract = {It is evident that rabies continues to be a neglected tropical disease;
   however, a recent global drive aims to eliminate canine-mediated human
   rabies by 2030. Global efforts have been vested into creating and
   developing resources for countries to take ownership of and overcome the
   challenges that rabies poses. The disconnect between the numbers of
   rabies cases reported and the numbers estimated by prediction models is
   clear: the key to understanding the epidemiology and true burden of
   rabies lies within accurate and timely data; poor and discrepant data
   undermine its true burden and negate the advocacy efforts needed to curb
   this lethal disease. In an effort to address these challenges, the
   Pan-African Rabies Control Network is developing a regional
   rabies-specific disease surveillance bulletin based on the District
   Health Information System 2 platform-a web-based, open access health
   information platform. This bulletin provides a data repository from
   which specific key indicators, essential to any rabies intervention
   program, form the basis of data collection. The data are automatically
   analyzed, providing useful outputs for targeted intervention.
   Furthermore, in an effort to reduce reporting fatigue, the data
   submitted, under authority from the respective governments, can
   automatically be shared with approved international authorities. The
   implementation of a rabies-specific bulletin will facilitate targeted
   control efforts and provide measurements of success, while also acting
   as a basis for advocacy to raise the priority of this neglected disease.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Nel, LH (Corresponding Author), Univ Pretoria, Dept Microbiol \& Plant Pathol, Fac Nat \& Agr Sci, Pretoria, South Africa.
   Nel, LH (Corresponding Author), Global Alliance Rabies Control, Manhattan, KS 66502 USA.
   Scott, Terence P.; Coetzer, Andre; Nel, Louis H., Univ Pretoria, Dept Microbiol \& Plant Pathol, Fac Nat \& Agr Sci, Pretoria, South Africa.
   Scott, Terence P.; Coetzer, Andre; Nel, Louis H., Global Alliance Rabies Control, Manhattan, KS 66502 USA.
   Fahrion, Anna S., WHO, Dept Control Neglected Trop Dis, Geneva, Switzerland.},
DOI = {10.3389/fvets.2017.00018},
Article-Number = {18},
EISSN = {2297-1769},
Keywords = {rabies; bulletin; DHIS2; data; surveillance; PARACON; reporting},
Keywords-Plus = {ELIMINATING CANINE RABIES; SURVEILLANCE},
Research-Areas = {Veterinary Sciences},
Web-of-Science-Categories  = {Veterinary Sciences},
Author-Email = {louis.nel@rabiesalliance.org},
Affiliations = {University of Pretoria; World Health Organization},
ResearcherID-Numbers = {Scott, Terence/J-8877-2019
   Nel, Louis H/F-1001-2012},
ORCID-Numbers = {Scott, Terence/0000-0001-5027-0031
   Nel, Louis H/0000-0001-8963-0153},
Funding-Acknowledgement = {UBS Optimus Foundation under the project Communities Against Rabies
   Exposures (CARE); Merial; Sanofi Pasteur; World Animal Protection under
   the project Catalysing Development of National Rabies Control Strategies},
Funding-Text = {The following organizations contributed financially toward this project:
   UBS Optimus Foundation under the project Communities Against Rabies
   Exposures (CARE); Merial and Sanofi Pasteur for their involvement and
   support in the PARACON Network and World Animal Protection under the
   project Catalysing Development of National Rabies Control Strategies.},
Number-of-Cited-References = {30},
Times-Cited = {21},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Front. Vet. Sci.},
Doc-Delivery-Number = {HC0DW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000451467500001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000722339400001,
Author = {Fekete, Alexander and Priesmeier, Peter},
Title = {Cross-Border Urban Change Detection and Growth Assessment for
   Mexican-USA Twin Cities},
Journal = {REMOTE SENSING},
Year = {2021},
Volume = {13},
Number = {21},
Month = {NOV},
Abstract = {Remote sensing applications of change detection are increasingly in
   demand for many areas of land use and urbanization, and disaster risk
   reduction. The Sendai Framework for Disaster Risk Reduction and the New
   Urban Agenda by the United Nations call for risk monitoring. This study
   maps and assesses the urban area changes of 23 Mexican-USA border cities
   with a remote sensing-based approach. A literature study on existing
   studies on hazard mapping and social vulnerability in those cities
   reveals a need for further studies on urban growth. Using a multi-modal
   combination of aerial, declassified (CORONA, GAMBIT, HEXAGON programs),
   and recent (Sentinel-2) satellite imagery, this study expands existing
   land cover change assessments by capturing urban growth back to the
   1940s. A Geographic Information System and census data assessment
   results reveal that massive urban growth has occurred on both sides of
   the national border. On the Mexican side, population and area growth
   exceeds the US cities in many cases. In addition, flood hazard exposure
   has grown along with growing city sizes, despite structural river
   training. These findings indicate a need for more risk monitoring that
   includes remote sensing data. It has socio-economic implications, too,
   as the social vulnerability on Mexican and US sides differ. This study
   calls for the maintenance and expansion of open data repositories to
   enable such transboundary risk comparisons. Common vulnerability
   variable sets could be helpful to enable better comparisons as well as
   comparable flood zonation mapping techniques. To enable risk monitoring,
   basic data such as urban boundaries should be mapped per decade and
   provided on open data platforms in GIS formats and not just in map
   viewers.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Fekete, A (Corresponding Author), TH Koln Univ Appl Sci, Inst Rescue Engn \& Civil Protect, Betzdorferstr 2, D-50679 Cologne, Germany.
   Fekete, Alexander; Priesmeier, Peter, TH Koln Univ Appl Sci, Inst Rescue Engn \& Civil Protect, Betzdorferstr 2, D-50679 Cologne, Germany.},
DOI = {10.3390/rs13214422},
Article-Number = {4422},
EISSN = {2072-4292},
Keywords = {aerial image; satellite imagery; change detection; land-use change;
   urban sprawl; decision-support; sister-cities; Sendai Framework; New
   Urban Agenda; risk monitoring},
Keywords-Plus = {LAND-COVER CLASSIFICATION; SOCIAL VULNERABILITY; TIME-SERIES;
   METROPOLITAN-AREA; SPATIAL STRUCTURE; CLIMATE-CHANGE; IMAGERY; RISK;
   DYNAMICS; HAZARDS},
Research-Areas = {Environmental Sciences \& Ecology; Geology; Remote Sensing; Imaging
   Science \& Photographic Technology},
Web-of-Science-Categories  = {Environmental Sciences; Geosciences, Multidisciplinary; Remote Sensing;
   Imaging Science \& Photographic Technology},
Author-Email = {alexander.fekete@th-koeln.de
   peter.priesmeier@th-koeln.de},
ResearcherID-Numbers = {Fekete, Alexander/C-4071-2017
   },
ORCID-Numbers = {Fekete, Alexander/0000-0002-8029-6774
   Priesmeier, Peter/0000-0001-7787-6447},
Number-of-Cited-References = {115},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {14},
Journal-ISO = {Remote Sens.},
Doc-Delivery-Number = {XC9OF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000722339400001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001009177400001,
Author = {Coelho, Flavio and Camara, Daniel Cardoso Portela and Araujo, Eduardo
   Correa and Bianchi, Lucas Monteiro and Ogasawara, Ivan and Dalal, Jyoti
   and James, Ananthu and Abbate, Jessica L. and Merzouki, Aziza and dos
   Reis, Izabel Cristina and Nwosu, Kene David and Keiser, Olivia},
Title = {A Platform for Data-Centric, Continuous Epidemiological Analyses
   (EpiGraphHub): Descriptive Analysis},
Journal = {JOURNAL OF MEDICAL INTERNET RESEARCH},
Year = {2023},
Volume = {25},
Month = {MAR 6},
Abstract = {Background: Guaranteeing durability, provenance, accessibility, and
   trust in open data sets can be challenging for researchers and
   organizations that rely on public repositories of data critical for
   epidemiology and other health analytics. The required data repositories
   are often difficult to locate and may require conversion to a standard
   data format. Data-hosting websites may also change or become unavailable
   without warning. A single change to the rules in one repository can
   hinder updating a public dashboard reliant on data pulled from external
   sources. These concerns are particularly challenging at the
   international level, because policies on systems aimed at harmonizing
   health and related data are typically dictated by national governments
   to serve their individual needs.
   Objective: In this paper, we introduce a comprehensive public health
   data platform, EpiGraphHub, that aims to provide a single interoperable
   repository for open health and related data.
   Methods: The platform, curated by the international research community,
   allows secure local integration of sensitive data while facilitating the
   development of data-driven applications and reports for decision-makers.
   Its main components include centrally managed databases with
   fine-grained access control to data, fully automated and documented data
   collection and transformation, and a powerful web-based data exploration
   and visualization tool.
   Results: EpiGraphHub is already being used for hosting a growing
   collection of open data sets and for automating epidemiological analyses
   based on them. The project has also released an open-source software
   library with the analytical methods used in the platform.
   Conclusions: The platform is fully open source and open to external
   users. It is in active development with the goal of maximizing its value
   for large-scale public health studies.},
Publisher = {JMIR PUBLICATIONS, INC},
Address = {130 QUEENS QUAY East, Unit 1100, TORONTO, ON M5A 0P6, CANADA},
Type = {Article},
Language = {English},
Affiliation = {Coelho, F (Corresponding Author), Fundacao Getulio Vargas, Sch Appl Math, Praia Botafogo 190 s508, BR-22250900 Rio De Janeiro, Brazil.
   Coelho, Flavio, Fundacao Getulio Vargas, Sch Appl Math, Rio De Janeiro, Brazil.
   Coelho, Flavio; Camara, Daniel Cardoso Portela; Araujo, Eduardo Correa; Bianchi, Lucas Monteiro; Ogasawara, Ivan; Dalal, Jyoti; James, Ananthu; Abbate, Jessica L.; Merzouki, Aziza; dos Reis, Izabel Cristina; Nwosu, Kene David; Keiser, Olivia, Global Res \& Anal Publ Hlth Network, Geneva, Switzerland.
   Camara, Daniel Cardoso Portela; dos Reis, Izabel Cristina, Fundacao Oswaldo Cruz, Lab Mosquitos Transmissores Hematozoarios, Inst Oswaldo Cruz, Rio De Janeiro, Brazil.
   Bianchi, Lucas Monteiro, Fundacao Oswaldo Cruz, Natl Publ Hlth Sch, Rio De Janeiro, Brazil.
   Abbate, Jessica L., Geomatys, Montpellier, France.
   Merzouki, Aziza; Keiser, Olivia, Univ Geneva, Inst Global Hlth, Fac Med, Geneva, Switzerland.},
DOI = {10.2196/40554},
Article-Number = {e40554},
ISSN = {1438-8871},
Keywords = {epidemiology; data analysis; disease surveillance; data science; public
   health; durability; accessibility; data set; public; platform; data;
   application; decision; decision-making},
Keywords-Plus = {COVID-19; TECHNOLOGY; FIGHT},
Research-Areas = {Health Care Sciences \& Services; Medical Informatics},
Web-of-Science-Categories  = {Health Care Sciences \& Services; Medical Informatics},
Author-Email = {fccoelho@fgv.br},
Affiliations = {Getulio Vargas Foundation; Escola de Pos-Graduacao em Economia (EPGE);
   Fundacao Oswaldo Cruz; Fundacao Oswaldo Cruz; University of Geneva},
ResearcherID-Numbers = {Camara, Daniel Cardoso Portela/S-3504-2018
   Coelho, Flavio/L-1089-2018
   },
ORCID-Numbers = {James, Ananthu/0000-0002-2562-347X
   Keiser, Olivia/0000-0001-8191-2789
   Camara, Daniel Cardoso Portela/0000-0002-5439-4477
   Coelho, Flavio/0000-0003-3868-4391
   Monteiro Bianchi, Lucas/0000-0001-7160-1143
   Correa Araujo, Eduardo/0000-0002-4032-6123
   Ogasawara, Ivan/0000-0001-5049-4289
   dos Reis, Izabel Cristina/0000-0002-1961-6556},
Funding-Acknowledgement = {Swiss National Science Foundation {[}31CA30\_196270, PP00P3\_202660];
   World Health Organization; Swiss National Science Foundation (SNF)
   {[}31CA30\_196270, PP00P3\_202660] Funding Source: Swiss National
   Science Foundation (SNF)},
Funding-Text = {Acknowledgments This project was supported by the Swiss National Science
   Foundation (grants 31CA30\_196270 and PP00P3\_202660) and the World
   Health Organization. We thank Sabina Rodriguez for editing the
   manuscript.},
Number-of-Cited-References = {36},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {J. Med. Internet Res.},
Doc-Delivery-Number = {J4FD7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001009177400001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000516139700001,
Author = {Bercic, Katja and Vidali, Janos},
Title = {DiscreteZOO: A Fingerprint Database of Discrete Objects},
Journal = {MATHEMATICS IN COMPUTER SCIENCE},
Year = {2020},
Volume = {14},
Number = {3, SI},
Pages = {559-575},
Month = {SEP},
Abstract = {In this paper, we present DiscreteZOO, a project which illustrates some
   of the possibilities for computer-supported management of collections of
   finite combinatorial (discrete) objects, in particular graphs with a
   high degree of symmetry. DiscreteZOO encompasses a data repository, a
   website and a SageMath Package.},
Publisher = {SPRINGER BASEL AG},
Address = {PICASSOPLATZ 4, BASEL, 4052, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Bercic, K (Corresponding Author), FAU Erlangen Nurnberg, Erlangen, Germany.
   Bercic, Katja, FAU Erlangen Nurnberg, Erlangen, Germany.
   Vidali, Janos, Univ Ljubljana, Fac Math \& Phys, Ljubljana, Slovenia.
   Vidali, Janos, Inst Math Phys \& Mech, Ljubljana, Slovenia.},
DOI = {10.1007/s11786-020-00453-5},
EarlyAccessDate = {FEB 2020},
ISSN = {1661-8270},
EISSN = {1661-8289},
Keywords = {Fingerprint database; Vertex-transitive graphs; Maniplexes; SageMath
   package; Website},
Keywords-Plus = {GRAPHS},
Research-Areas = {Mathematics},
Web-of-Science-Categories  = {Mathematics, Applied},
Author-Email = {katja.bercic@fau.de
   janos.vidali@fmf.uni-lj.si},
Affiliations = {University of Erlangen Nuremberg; University of Ljubljana},
ResearcherID-Numbers = {Vidali, Janoš/AAH-2383-2020
   },
ORCID-Numbers = {Vidali, Janoš/0000-0001-8061-9169
   Bercic, Katja/0000-0002-6678-8975},
Funding-Acknowledgement = {Projekt DEAL; OpenDreamKit Horizon 2020 European Research
   Infrastructures project {[}676541]; Slovenian Research Agency
   {[}P1-0285, J1-8130]},
Funding-Text = {Open Access funding provided by Projekt DEAL. The work by the first
   author reported here is supported in part by the OpenDreamKit Horizon
   2020 European Research Infrastructures project (\#676541). The first
   author did the main portion of her work on the project while a
   postdoctoral scholar at the Center for Mathematical Sciences of the
   National Autonomous University of Mexico, Campus Morelia. The work by
   the second author reported here is supported by the Slovenian Research
   Agency (research program P1-0285 and project J1-8130). The first author
   would also like to thank Michael Kohlhase for his encouragement, his
   many insightful comments, and for pointing out the need to include a
   checksum in a CID. Finally, the authors would like to thank the second
   reviewer for important comments.},
Number-of-Cited-References = {35},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Math. Comput. Sci.},
Doc-Delivery-Number = {MX8WA},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000516139700001},
OA = {Green Published, Green Submitted, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000604422700001,
Author = {Qureshi, Muhammad Sajid and Daud, Ali and Hayat, Malik Khizar and Afzal,
   Muhammad Tanvir},
Title = {OpenRank - a novel approach to rank universities using objective and
   publicly verifiable data sources},
Journal = {LIBRARY HI TECH},
Year = {2023},
Volume = {41},
Number = {2},
Pages = {474-500},
Month = {JUN 1},
Abstract = {Purpose Academic rankings are facing various issues, including the use
   of data sources that are not publicly verifiable, subjective parameters,
   a narrow focus on research productivity and regional biases and so
   forth. This research work is intended to enhance creditability of the
   ranking process by using the objective indicators based on publicly
   verifiable data sources. Design/methodology/approach The proposed
   ranking methodology - OpenRank - drives the objective indicators from
   two well-known publicly verifiable data repositories: the ArnetMiner and
   DBpedia. Findings The resultant academic ranking reflects common
   tendencies of the international academic rankings published by the
   Shanghai Ranking Consultancy (SRC), Quacquarelli Symonds (QS) and Times
   Higher Education (THE). Evaluation of the proposed methodology advocates
   its effectiveness and quick reproducibility with low cost of data
   collection. Research limitations/implications Implementation of the
   OpenRank methodology faced the issue of availability of the quality
   data. In future, accuracy of the academic rankings can be improved
   further by employing more relevant public data sources like the
   Microsoft Academic Graph, millions of graduate's profiles available in
   the LinkedIn repositories and the bibliographic data maintained by
   Association for Computing Machinery and Scopus and so forth. Practical
   implications The suggested use of open data sources would offer new
   dimensions to evaluate academic performance of the higher education
   institutions (HEIs) and having comprehensive understanding of the
   catalyst factors in the higher education. Social implications The
   research work highlighted the need of a purposely built, publicly
   verifiable electronic data source for performance evaluation of the
   global HEIs. Availability of such a global database would help in better
   academic planning, monitoring and analysis. Definitely, more
   transparent, reliable and less controversial academic rankings can be
   generated by employing the aspired data source. Originality/value We
   suggested a satisfying solution for improvement of the HEIs' ranking
   process by making the following contributions: (1) enhancing
   creditability of the ranking results by merely employing the objective
   performance indicators extracted from the publicly verifiable data
   sources, (2) developing an academic ranking methodology based on the
   objective indicators using two well-known data repositories, the DBpedia
   and ArnetMiner and (3) demonstrating effectiveness of the proposed
   ranking methodology on the real data sources.},
Publisher = {EMERALD GROUP PUBLISHING LTD},
Address = {HOWARD HOUSE, WAGON LANE, BINGLEY BD16 1WA, W YORKSHIRE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Qureshi, MS (Corresponding Author), Int Islamic Univ, Dept Comp Sci \& Software Engn, Islamabad, Pakistan.
   Qureshi, MS (Corresponding Author), Fdn Univ Islamabad, Dept Software Engn, Rawalpindi, Pakistan.
   Qureshi, Muhammad Sajid; Daud, Ali, Int Islamic Univ, Dept Comp Sci \& Software Engn, Islamabad, Pakistan.
   Qureshi, Muhammad Sajid, Fdn Univ Islamabad, Dept Software Engn, Rawalpindi, Pakistan.
   Daud, Ali, Univ Jeddah, Coll Comp Sci \& Engn, Dept Comp Sci \& Artificial Intelligence, Jeddah, Saudi Arabia.
   Hayat, Malik Khizar, Univ Haripur, Fac Informat Technol \& Engn, Dept Informat Technol, Haripur, Pakistan.
   Afzal, Muhammad Tanvir, NAMAL Inst, Dept Comp Sci, Mianwali, Pakistan.},
DOI = {10.1108/LHT-07-2019-0131},
EarlyAccessDate = {JAN 2021},
ISSN = {0737-8831},
Keywords = {Academic rankings; Information retrieval; Linked Data Cloud; DBpedia;
   ArnetMiner; Linked data},
Research-Areas = {Information Science \& Library Science},
Web-of-Science-Categories  = {Information Science \& Library Science},
Author-Email = {sajid.phdcs99@iiu.edu.pk
   ali.daud@iiu.edu.pk
   khizar.malik@fui.edu.pk
   mafzal@cust.edu.pk},
Affiliations = {International Islamic University, Pakistan; University of Jeddah},
ResearcherID-Numbers = {Hayat, Malik Khizar/AAH-4881-2020
   Daud, Ali/ABA-8422-2020},
ORCID-Numbers = {Hayat, Malik Khizar/0000-0001-8177-2042
   Daud, Ali/0000-0002-8284-6354},
Number-of-Cited-References = {38},
Times-Cited = {3},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {28},
Journal-ISO = {Libr. Hi Tech},
Doc-Delivery-Number = {H9WA9},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000604422700001},
DA = {2024-01-15},
}

@article{ WOS:000443882300005,
Author = {Fast, Victoria and Rinner, Claus},
Title = {Toward a participatory VGI methodology: crowdsourcing information on
   regional food assets},
Journal = {INTERNATIONAL JOURNAL OF GEOGRAPHICAL INFORMATION SCIENCE},
Year = {2018},
Volume = {32},
Number = {11},
Pages = {2209-2224},
Abstract = {Local knowledge has been underrepresented in food-related policies and
   planning. The goal of this research was to engage members of a local
   food community and generate volunteered geographic information (VGI) on
   community food assets. During active data collection, over 200 food
   assets were reported. This paper details the systematic approach used to
   create VGI, which emphasizes the socio-cultural context surrounding the
   mapping technology. The project began with an identified need to connect
   to and learn from the local food community. The participants were drawn
   from active food system stakeholders, and a Geoweb infrastructure was
   selected based on publicly available crowdsourcing tools. The resulting
   VGI is presented according to system functions: input (Web traffic,
   contributors, input types), management (contribution vetting, privacy),
   analysis (typology of input), and presentation (sharing the submitted
   data). Despite limitations, this study revealed a hyper-local and
   community-driven perspective on food assets, opened access to government
   and private data, and increased the transparency and accessibility of
   information on the regional food system. This research also revealed
   that there is a growing need for intermediaries who can bridge the gap
   between experts in the subject matter and experts in digitally enabled
   participation, and a need for non-government open data repositories.},
Publisher = {TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Fast, V (Corresponding Author), Univ Calgary, Dept Geog, Calgary, AB, Canada.
   Fast, Victoria, Univ Calgary, Dept Geog, Calgary, AB, Canada.
   Rinner, Claus, Ryerson Univ, Dept Geog \& Environm Studies, Toronto, ON, Canada.},
DOI = {10.1080/13658816.2018.1480784},
ISSN = {1365-8816},
EISSN = {1362-3087},
Keywords = {Public participation GIS; community engagement; food systems; urban
   applications},
Keywords-Plus = {VOLUNTEERED GEOGRAPHIC INFORMATION; PUBLIC-PARTICIPATION; SYSTEMS},
Research-Areas = {Computer Science; Geography; Physical Geography; Information Science \&
   Library Science},
Web-of-Science-Categories  = {Computer Science, Information Systems; Geography; Geography, Physical;
   Information Science \& Library Science},
Author-Email = {victoria.fast@ucalgary.ca},
Affiliations = {University of Calgary; Toronto Metropolitan University},
ORCID-Numbers = {Fast, Victoria/0000-0002-7093-3864},
Funding-Acknowledgement = {Social Sciences and Humanities Research Council of Canada Geothink
   Project {[}SSHRC 895-2012-1023]; Social Sciences and Humanities Research
   Council of Canada Joseph-Armand Bombardier CGS Doctoral Scholarship},
Funding-Text = {This work was supported by the Social Sciences and Humanities Research
   Council of Canada Geothink Project: SSHRC 895-2012-1023 and Social
   Sciences and Humanities Research Council of Canada Joseph-Armand
   Bombardier CGS Doctoral Scholarship.},
Number-of-Cited-References = {46},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {21},
Journal-ISO = {Int. J. Geogr. Inf. Sci.},
Doc-Delivery-Number = {GS7LK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000443882300005},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000406391200213,
Author = {Grellier, James and White, Mathew P. and Albin, Maria and Bell, Simon
   and Elliott, Lewis R. and Gascon, Mireia and Gualdi, Silvio and Mancini,
   Laura and Nieuwenhuijsen, Mark J. and Sarigiannis, Denis A. and van den
   Bosch, Matilda and Wolf, Tanja and Wuijts, Susanne and Fleming, Lora E.},
Title = {BlueHealth: a study programme protocol for mapping and quantifying the
   potential benefits to public health and well-being from Europe's blue
   spaces},
Journal = {BMJ OPEN},
Year = {2017},
Volume = {7},
Number = {6},
Month = {JUN},
Abstract = {Introduction Proximity and access to water have long been central to
   human culture and accordingly deliver countless societal benefits. Over
   200 million people live on Europe's coastline, and aquatic environments
   are the top recreational destination in the region. In terms of public
   health, interactions with `blue space' (eg, coasts, rivers, lakes) are
   often considered solely in terms of risk (eg, drowning, microbial
   pollution). Exposure to blue space can, however, promote health and
   well-being and prevent disease, although underlying mechanisms are
   poorly understood.
   Aims and methods The BlueHealth project aims to understand the
   relationships between exposure to blue space and health and well-being,
   to map and quantify the public health impacts of changes to both natural
   blue spaces and associated urban infrastructure in Europe, and to
   provide evidence-based information to policymakers on how to maximise
   health benefits associated with interventions in and around aquatic
   environments. To achieve these aims, an evidence base will be created
   through systematic reviews, analyses of secondary data sets and analyses
   of new data collected through a bespoke international survey and a wide
   range of community-level interventions. We will also explore how to
   deliver the benefits associated with blue spaces to those without direct
   access through the use of virtual reality. Scenarios will be developed
   that allow the evaluation of health impacts in plausible future societal
   contexts and changing environments. BlueHealth will develop key inputs
   into policymaking and land/water-use planning towards more salutogenic
   and sustainable uses of blue space, particularly in urban areas.
   Ethics and dissemination Throughout the BlueHealth project, ethics
   review and approval are obtained for all relevant aspects of the study
   by the local ethics committees prior to any work being initiated and an
   ethics expert has been appointed to the project advisory board. So far,
   ethical approval has been obtained for the BlueHealth International
   Survey and for community-level interventions taking place in Spain,
   Italy and the UK. Engagement of stakeholders, including the public,
   involves citizens in many aspects of the project. Results of all
   individual studies within the BlueHealth project will be published with
   open access. After full anonymisation and application of any measures
   necessary to prevent disclosure, data generated in the project will be
   deposited into open data repositories of the partner institutions, in
   line with a formal data management plan. Other knowledge and tools
   developed in the project will be made available via the project website
   (www.bluehealth2020.eu). Project results will ultimately provide key
   inputs to planning and policy relating to blue space, further
   stimulating the integration of environmental and health considerations
   into decision-making, such that blue infrastructure is developed across
   Europe with both public health and the environment in mind.},
Publisher = {BMJ PUBLISHING GROUP},
Address = {BRITISH MED ASSOC HOUSE, TAVISTOCK SQUARE, LONDON WC1H 9JR, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Grellier, J (Corresponding Author), Univ Exeter, Med Sch, ECEHH, Truro, England.
   Grellier, J (Corresponding Author), Imperial Coll, Sch Publ Hlth, Fac Med, London, England.
   Grellier, James; White, Mathew P.; Elliott, Lewis R.; Fleming, Lora E., Univ Exeter, Med Sch, ECEHH, Truro, England.
   Grellier, James, Imperial Coll, Sch Publ Hlth, Fac Med, London, England.
   White, Mathew P.; Elliott, Lewis R., Univ Exeter, Med Sch, PAtH, Exeter, Devon, England.
   Albin, Maria, Lund Univ, Dept Lab Med, OEM, Lund, Sweden.
   Albin, Maria, Karolinska Inst, Inst Environm Med IMM, Stockholm, Sweden.
   Bell, Simon, Estonian Univ Life Sci, Dept Landscape Architect, Tartu, Estonia.
   Bell, Simon, Univ Edinburgh, Edinburgh Coll Art, OPENspace, Edinburgh, Midlothian, Scotland.
   Gascon, Mireia; Nieuwenhuijsen, Mark J., Univ Barcelona, Hosp Clin, Inst Salud Global Barcelona ISGlobal, Ctr Int Hlth Res CRESIB, Barcelona, Spain.
   Gascon, Mireia; Nieuwenhuijsen, Mark J., Inst Salud Global Barcelona ISGlobal, Ctr Res Environm Epidemiol CREAL, Barcelona, Spain.
   Gascon, Mireia; Nieuwenhuijsen, Mark J., Univ Pompeu Fabra UPF, Barcelona, Spain.
   Gascon, Mireia; Nieuwenhuijsen, Mark J., CIBERESP, Barcelona, Spain.
   Gualdi, Silvio, Fdn Ctr Euromediterraneo Cambiamenti Climat CMCC, Bologna, Italy.
   Mancini, Laura, ISS, Rome, Italy.
   Sarigiannis, Denis A., Aristotle Univ Thessaloniki AUTH, Thessaloniki, Greece.
   van den Bosch, Matilda, Univ British Columbia, Fac Forestry, Dept Forest \& Conservat Sci, Vancouver, BC, Canada.
   van den Bosch, Matilda, WHO, Reg Off Europe, European Ctr Environm \& Hlth, Bonn, Germany.
   van den Bosch, Matilda; Wolf, Tanja, Univ British Columbia, Fac Med, Sch Populat \& Publ Hlth, Vancouver, BC, Canada.
   Wuijts, Susanne, Natl Inst Publ Hlth \& Environm RIVM, Bilthoven, Netherlands.},
DOI = {10.1136/bmjopen-2017-016188},
Article-Number = {e016188},
ISSN = {2044-6055},
Keywords-Plus = {URBAN WATERFRONT REGENERATION; NATURAL ENVIRONMENTS; COASTAL PROXIMITY;
   PHYSICAL-ACTIVITY; CLIMATE-CHANGE; EXPOSURE; GREEN; FRAMEWORK; IMPACTS;
   DESIGN},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {j.grellier@exeter.ac.uk},
Affiliations = {University of Exeter; Imperial College London; University of Exeter;
   Lund University; Karolinska Institutet; Estonian University of Life
   Sciences; Edinburgh College of Art; University of Edinburgh; University
   of Barcelona; Hospital Clinic de Barcelona; ISGlobal; CRESIB; ISGlobal;
   Pompeu Fabra University; Pompeu Fabra University; CIBER - Centro de
   Investigacion Biomedica en Red; CIBERESP; Centro Euro-Mediterraneo sui
   Cambiamenti Climatici (CMCC); Istituto Superiore di Sanita (ISS);
   Aristotle University of Thessaloniki; University of British Columbia;
   World Health Organization; University of British Columbia; Netherlands
   National Institute for Public Health \& the Environment},
ResearcherID-Numbers = {Sarigiannis, Denis/AAD-4251-2019
   Nieuwenhuijsen, Mark J/C-3914-2017
   Grellier, James/Q-9557-2016
   Gascon, Mireia/G-1275-2016
   Gualdi, Silvio/F-3061-2015
   White, Mathew P/AAZ-4113-2021
   Albin, Maria/HJI-3265-2023
   Fleming, Lora E/ABH-1310-2021
   van den Bosch, Matilda/F-1550-2013
   },
ORCID-Numbers = {Nieuwenhuijsen, Mark J/0000-0001-9461-7981
   Grellier, James/0000-0002-7458-7479
   Gascon, Mireia/0000-0003-4537-8472
   Gualdi, Silvio/0000-0001-7777-8935
   Fleming, Lora E/0000-0003-1076-9967
   Albin, Maria/0000-0002-6613-4437
   SARIGIANNIS, DIMOSTHENIS/0000-0003-2514-314X
   mancini, laura/0000-0003-3667-5221
   Bell, Simon/0000-0002-0986-3887
   Elliott, Lewis/0000-0003-3864-9465
   van den Bosch, Matilda/0000-0003-1410-0099
   White, Mathew Philip/0000-0002-4168-7289},
Funding-Acknowledgement = {European Union's Horizon research and innovation programme {[}666773]},
Funding-Text = {This work was supported by funding received from the European Union's
   Horizon 2020 research and innovation programme under grant agreement no.
   666773.},
Number-of-Cited-References = {92},
Times-Cited = {137},
Usage-Count-Last-180-days = {17},
Usage-Count-Since-2013 = {144},
Journal-ISO = {BMJ Open},
Doc-Delivery-Number = {FB8LT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000406391200213},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000866242600001,
Author = {Seider, Jordan H. and Lantz, Trevor C. and Bone, Christopher},
Title = {Tundra shrub expansion in a warming climate and the influence of data
   type on models of habitat suitability},
Journal = {ARCTIC ANTARCTIC AND ALPINE RESEARCH},
Year = {2022},
Volume = {54},
Number = {1},
Pages = {488-506},
Month = {DEC 31},
Abstract = {Warming across the low Arctic is increasing tundra vegetation
   productivity and facilitating the expansion of upright shrubs. We
   modeled the effects of warming on habitat suitability in green alder,
   dwarf birch, Labrador tea, bog bilberry, and lingonberry and assessed
   the influence of data type (true absence or pseudo-absence) on species
   distribution models (SDMs). We generated SDMs using the two absence data
   types under current (1970-2000) and future (2061-2080) climate
   projections. Our results show that warming leads to range expansion of
   all shrubs, though responses vary in magnitude and extent, with mean
   increases in suitability ranging from 0.080 (Labrador tea) to 0.369
   (lingonberry) with true absences. Differences in driving variables and
   suitability projections suggest that physiological and ecological
   variability between species mediate responses to warming. Between data
   types, we observed inconsistencies in model performance, suitability
   projections, and variable importance. Bog bilberry and lingonberry
   exhibited larger differences in suitability (0.201 and 0.288,
   respectively), whereas alder showed similar responses (difference of
   0.01). These results are important to consider when assessing changes in
   habitat suitability or identifying environmental or climatic
   determinants of species' distributions. We suggest further development
   of open data repositories, facilitating access to true absence data to
   support conservation and land use planning.},
Publisher = {TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Lantz, TC (Corresponding Author), Univ Victoria, Sch Environm Studies, POB 1700 STN CSC, Victoria, BC V8W 2Y2, Canada.
   Seider, Jordan H.; Lantz, Trevor C., Univ Victoria, Sch Environm Studies, POB 1700 STN CSC, Victoria, BC V8W 2Y2, Canada.
   Bone, Christopher, Univ Victoria, Dept Geog, Victoria, BC, Canada.},
DOI = {10.1080/15230430.2022.2121243},
ISSN = {1523-0430},
EISSN = {1938-4246},
Keywords = {Tundra; shrubs; climate change; species distribution modeling;
   pseudo-absence},
Keywords-Plus = {SPECIES DISTRIBUTION MODELS; PLANT FUNCTIONAL TYPES;
   VACCINIUM-VITIS-IDAEA; VEGETATION DYNAMICS; PRESENCE-ABSENCE; GROWTH;
   DISTRIBUTIONS; FEEDBACKS; INFORMATION; ENVIRONMENT},
Research-Areas = {Environmental Sciences \& Ecology; Physical Geography},
Web-of-Science-Categories  = {Environmental Sciences; Geography, Physical},
Author-Email = {tlantz@uvic.ca},
Affiliations = {University of Victoria; University of Victoria},
ORCID-Numbers = {Seider, Jordan/0000-0002-6329-5833},
Funding-Acknowledgement = {Natural Sciences and Engineering Research Council of Canada
   {[}06210-2018]; Northern Scientific Training Program; Polar Continental
   Shelf Program; University of Victoria; Aurora Research Institute},
Funding-Text = {Funding for this research was provided by the Natural Sciences and
   Engineering Research Council of Canada (Discovery Grant 06210-2018 to
   TCL and a Canada Graduate Scholarship Award to JHS), the Northern
   Scientific Training Program, the Polar Continental Shelf Program, the
   Aurora Research Institute, and the University of Victoria.},
Number-of-Cited-References = {120},
Times-Cited = {0},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Arct. Antarct. Alp. Res.},
Doc-Delivery-Number = {5F3TY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000866242600001},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000516827000072,
Author = {Cocca, Michele and Teixeira, Douglas and Vassio, Luca and Mellia, Marco
   and Almeida, Jussara M. and Couto da Silva, Ana Paula},
Title = {On Car-Sharing Usage Prediction with Open Socio-Demographic Data},
Journal = {ELECTRONICS},
Year = {2020},
Volume = {9},
Number = {1},
Month = {JAN},
Abstract = {Free-Floating Car-Sharing (FFCS) services are a flexible alternative to
   car ownership. These transportation services show highly dynamic usage
   both over different hours of the day, and across different city areas.
   In this work, we study the problem of predicting FFCS demand patterns-a
   problem of great importance to the adequate provisioning of the service.
   We tackle both the prediction of the demand (i) over time and (ii) over
   space. We rely on months of real FFCS rides in Vancouver, which
   constitute our ground truth. We enrich this data with detailed
   socio-demographic information obtained from large open-data repositories
   to predict usage patterns. Our aim is to offer a thorough comparison of
   several machine-learning algorithms in terms of accuracy and ease of
   training, and to assess the effectiveness of current state-of-the-art
   approaches to address the prediction problem. Our results show that it
   is possible to predict the future usage with relative errors down to
   10\%, while the spatial prediction can be estimated with relative errors
   of about 40\%. Our study also uncovers the socio-demographic features
   that most strongly correlate with FFCS usage, providing interesting
   insights for providers interested in offering services in new regions.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Cocca, M (Corresponding Author), Politecn Torino, Dept Elect \& Telecommun, I-10129 Turin, TO, Italy.
   Cocca, Michele; Vassio, Luca; Mellia, Marco, Politecn Torino, Dept Elect \& Telecommun, I-10129 Turin, TO, Italy.
   Teixeira, Douglas; Almeida, Jussara M.; Couto da Silva, Ana Paula, Univ Fed Minas Gerais, Dept Ciencia Comp, BR-31270901 Belo Horizonte, MG, Brazil.},
DOI = {10.3390/electronics9010072},
Article-Number = {72},
EISSN = {2079-9292},
Keywords = {Machine Learning; Regression models; Car Sharing},
Research-Areas = {Computer Science; Engineering; Physics},
Web-of-Science-Categories  = {Computer Science, Information Systems; Engineering, Electrical \&
   Electronic; Physics, Applied},
Author-Email = {michele.cocca@polito.it
   douglas@dcc.ufmg.br
   luca.vassio@polito.it
   marco.mellia@polito.it
   jussara@dcc.ufmg.br
   ana.coutosilva@dcc.ufmg.br},
Affiliations = {Polytechnic University of Turin; Universidade Federal de Minas Gerais},
ResearcherID-Numbers = {Silva, Ana/JGM-6679-2023
   Vassio, Luca/X-7386-2019
   Almeida, Jussara M/AAD-4947-2022
   Mellia, Marco/G-7997-2018
   da Silva, Ana/GXH-4851-2022
   },
ORCID-Numbers = {Vassio, Luca/0000-0002-2920-1856
   Mellia, Marco/0000-0003-1859-6693
   Cocca, Michele/0000-0002-7574-128X
   Teixeira, Douglas/0000-0003-2804-063X},
Funding-Acknowledgement = {Compagnia di San Paolo; Brazilian research agency CNPq; Brazilian
   research agency CAPES; Brazilian research agency FAPEMIG;
   SmartData@Politocenter},
Funding-Text = {The research leading to these results has been funded by the Compagnia
   di San Paolo through the 2019 internationalisation project program
   between Politecnico di Torino (Italy) and Universidade Federal de Minas
   Gerais (Brazil), by the Brazilian research agencies CNPq, CAPES and
   FAPEMIG, and by the SmartData@Politocenter.},
Number-of-Cited-References = {22},
Times-Cited = {14},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Electronics},
Doc-Delivery-Number = {KQ3LC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000516827000072},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000851846500001,
Author = {Houssein, Essam H. and Ibrahem, Nahed and Zaki, Alaa M. and Sayed, Awny},
Title = {Semantic Protocol and Resource Description Framework Query Language: A
   Comprehensive Review},
Journal = {MATHEMATICS},
Year = {2022},
Volume = {10},
Number = {17},
Month = {SEP},
Abstract = {This review presents various perspectives on converting user keywords
   into a formal query. Without understanding the dataset's underlying
   structure, how can a user input a text-based query and then convert this
   text into semantic protocol and resource description framework query
   language (SPARQL) that deals with the resource description framework
   (RDF) knowledge base? The user may not know the structure and syntax of
   SPARQL, a formal query language and a sophisticated tool for the
   semantic web (SEW) and its vast and growing collection of interconnected
   open data repositories. As a result, this study examines various
   strategies for turning natural language into formal queries, their
   workings, and their results. In an Internet search engine from a single
   query, such as on Google, numerous matching documents are returned, with
   several related to the inquiry while others are not. Since a
   considerable percentage of the information retrieved is likely
   unrelated, sophisticated information retrieval systems based on SEW
   technologies, such as RDF and web ontology language (OWL), can help end
   users organize vast amounts of data to address this issue. This study
   reviews this research field and discusses two different approaches to
   show how users with no knowledge of the syntax of semantic web
   technologies deal with queries.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Houssein, EH (Corresponding Author), Minia Univ, Fac Comp \& Informat, Al Minya 61519, Egypt.
   Houssein, Essam H.; Ibrahem, Nahed, Minia Univ, Fac Comp \& Informat, Al Minya 61519, Egypt.
   Zaki, Alaa M., Minia Univ, Fac Sci, Al Minya 61519, Egypt.
   Sayed, Awny, King Abdulaziz Univ, Fac Comp \& Informat Technol, Informat Technol Dept, Jeddah 21589, Saudi Arabia.},
DOI = {10.3390/math10173203},
Article-Number = {3203},
EISSN = {2227-7390},
Keywords = {semantic web; SPARQL query; resource description framework (RDF);
   question answering system (QAS); semantic question answering (SQA); web
   ontology language (OWL)},
Keywords-Plus = {WEB; KNOWLEDGE; KEYWORDS; SEARCH},
Research-Areas = {Mathematics},
Web-of-Science-Categories  = {Mathematics},
Author-Email = {essam.halim@mu.edu.eg},
Affiliations = {Egyptian Knowledge Bank (EKB); Minia University; Egyptian Knowledge Bank
   (EKB); Minia University; King Abdulaziz University},
ResearcherID-Numbers = {Houssein, Essam Halim/C-8941-2016
   },
ORCID-Numbers = {Houssein, Essam Halim/0000-0002-8127-7233
   zaki, Alaa/0000-0002-2472-9774},
Number-of-Cited-References = {108},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Mathematics},
Doc-Delivery-Number = {4K3HX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000851846500001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:001025997100001,
Author = {Jia, Keren and Chen, Yang and Xie, Yi and Chong, Xiaoyi and Li, Yilin
   and Wu, Yingcheng and Yuan, Jiajia and Li, Yanyan and Feng, Xujiao and
   Hu, Yajie and Sun, Yu and Gong, Jifang and Zhang, Xiaotian and Li, Jian
   and Shen, Lin},
Title = {Multidimensional immune profiling in Gastric Cancer Multiplex
   Immunohistochemistry Atlas from Peking University Cancer Hospital
   project informs PD-1/PD-L1 blockade efficacy},
Journal = {EUROPEAN JOURNAL OF CANCER},
Year = {2023},
Volume = {189},
Month = {AUG},
Abstract = {Background: Immunotherapy has resulted in impressive objective response
   rates and durable tumour remission, but only in a subset of gastric
   cancer (GC) patients. The PD L1 combined positive score is the most
   widely used tissue-based biomarker for anti-PD-1/PDL1 therapy; however,
   this unidimensional method has limitations. Next-generation exploration
   of tissue-based biomarkers for GC requires characterisation of various
   cellular markers and key immunoregulatory molecule expression in situ.
   Thus, a complete, stepwise solution covering the entire process from
   staining samples to cross-site utilisation of pathomics data is urgently
   needed. Methods: With the advanced multispectral imaging analysis
   method, web-based data repository, and interactive sharing technology,
   we conducted a project entitled Gastric Cancer Multiplex
   Immunohistochemistry Atlas from Peking University Cancer Hospital
   (GMAP). We propose a standard pipeline covering sample collection,
   staining, scanning multispectral images, constructing a spectral
   library, identifying and phenotyping cells, positioning each element,
   and quantitatively extracting immune features. We designed an
   open-access relational database to explore tissue-based biomarkers to
   determine PD-1/PD-L1 blockade efficacy.Results: The GMAP project
   detected the functional status and spatial location of more than 50
   million cells using 15 markers in 80 GC patients, based on which
   billions of cell pairs were recognised, highlighting the rich spatial
   arrangement information and the fine tumour microenvironment structure.
   We generated a tumour-immune atlas using the count and spatial features
   of 65 immune cell types. We eventually selected the indicators and built
   a comprehensive risk-scoring system. Patients with higher risk score
   showed superior immunotherapyrelated progression-free survival (irPFS)
   (hazard ratio {[}HR]: 3.19; P < 0.001; median irPFS: 4.87 versus 19.87
   months, respectively) and immunotherapy-related overall survival (HR:
   3.10; P = 0.001; median irPFS: 10.03 versus 24.87 months, respectively)
   compared with lower risk patients, demonstrating their potential for
   guiding anti-PD-1/PD-L1-based immunotherapy. Importantly, an easy-to-use
   and versatile web server was built to promote tissue-based biomarker
   exploration in GC.Conclusion: The GMAP project highlighted the clinical
   value of tissue-based immune features as biomarkers for
   immunotherapeutic decision-making. We present a well-designed, detailed
   workflow for the orderly generation and use of a high-quality, spatially
   resolved pathological database.\& COPY; 2023 The Author(s). Published by
   Elsevier Ltd. This is an open access article under the CC BY-NC-ND
   license (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Shen, L (Corresponding Author), Peking Univ Canc Hosp \& Inst, Minist Educ, Dept Gastrointestinal Oncol, Key Lab Carcinogenesis \& Translat Res, Beijing, Peoples R China.
   Jia, Keren; Chen, Yang; Xie, Yi; Chong, Xiaoyi; Li, Yilin; Yuan, Jiajia; Li, Yanyan; Feng, Xujiao; Hu, Yajie; Gong, Jifang; Zhang, Xiaotian; Li, Jian; Shen, Lin, Peking Univ Canc Hosp \& Inst, Minist Educ, Dept Gastrointestinal Oncol, Key Lab Carcinogenesis \& Translat Res, Beijing, Peoples R China.
   Wu, Yingcheng, Fudan Univ, Zhongshan Hosp, Liver Canc Inst, Dept Liver Surg \& Transplantat, Shanghai, Peoples R China.
   Wu, Yingcheng, Fudan Univ, Zhongshan Hosp, Liver Canc Inst, Key Lab Carcinogenesis \& Canc Invas,Minist Educ, Shanghai, Peoples R China.
   Sun, Yu, Peking Univ Canc Hosp \& Inst, Minist Educ, Dept Pathol, Key Lab Carcinogenesis \& Translat Res, Beijing, Peoples R China.},
DOI = {10.1016/j.ejca.2023.05.019},
EarlyAccessDate = {JUN 2023},
Article-Number = {112931},
ISSN = {0959-8049},
EISSN = {1879-0852},
Keywords = {Gastric cancer; Immune feature; Immunotherapy; Pathomics; Biomarker},
Keywords-Plus = {T-CELL EXHAUSTION; GASTROESOPHAGEAL JUNCTION; PD-L1; CHEMOTHERAPY;
   INFECTION; NIVOLUMAB},
Research-Areas = {Oncology},
Web-of-Science-Categories  = {Oncology},
Author-Email = {shenlin@bjmu.edu.cn},
Affiliations = {Peking University; Fudan University; Fudan University; Peking University},
ResearcherID-Numbers = {Chen, Yang/JVN-3402-2024
   Li, Yilin/JCD-8027-2023
   Shen, Lin/JPX-7656-2023
   },
ORCID-Numbers = {Jia, Keren/0000-0001-6577-0573},
Funding-Acknowledgement = {National Natural Science Foundation of China {[}91959205, 82203881,
   U22A20327]; Beijing Natural Science Foundation {[}7222021, Z200015];
   Beijing Hospitals Authority Youth Programme {[}QML20231115]; Wu Jieping
   Medical Foundation {[}320.6750.2021-02-15]; Clinical Medicine Plus
   X-Young Scholars Project of Peking University {[}PKU2023LCXQ041]},
Funding-Text = {This work was supported by the National Natural Science Foundation of
   China {[}grant numbers 91959205, 82203881, U22A20327], the Beijing
   Natural Science Foundation {[}grant numbers 7222021, Z200015], Beijing
   Hospitals Authority Youth Programme, code {[}QML20231115], Wu Jieping
   Medical Foundation {[}grant numbers 320.6750.2021-02-15]. Clinical
   Medicine Plus X-Young Scholars Project of Peking University
   (PKU2023LCXQ041).},
Number-of-Cited-References = {50},
Times-Cited = {0},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Eur. J. Cancer},
Doc-Delivery-Number = {L8VW7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001025997100001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000644829600002,
Author = {Lanzano, Giovanni and Luzi, Lucia and Cauzzi, Carlo and Bienkowski,
   Jarek and Bindi, Dino and Clinton, John and Cocco, Massimo and D'Amico,
   Maria and Douglas, John and Faenza, Licia and Felicetta, Chiara and
   Gallovic, Frantisek and Giardini, Domenico and Ktenidou, Olga-Joan and
   Lauciani, Valentino and Manakou, Maria and Marmureanu, Alexandru and
   Maufroy, Emeline and Michelini, Alberto and Ozener, Haluk and Puglia,
   Rodolfo and Rupakhety, Rajesh and Russo, Emiliano and Shahvar, Mohammad
   and Sleeman, Reinoud and Theodoulidis, Nikolaos},
Title = {Accessing European Strong-Motion Data : An Update on ORFEUS Coordinated
   Services},
Journal = {SEISMOLOGICAL RESEARCH LETTERS},
Year = {2021},
Volume = {92},
Number = {3},
Pages = {1642-1658},
Month = {MAY},
Abstract = {Strong ground motion records and free open access to strong-motion data
   repositories are fundamental inputs to seismology, engineering
   seismology, soil dynamics, and earthquake engineering science and
   practice. This article presents the current status and outlook of the
   Observatories and Research Facilities for European Seismology (ORFEUS)
   coordinated strong-motion seismology services, namely the rapid raw
   strong-motion (RRSM) and the engineering strong-motion (ESM) databases
   and associated web interfaces and webservices. We compare and discuss
   the role and use of these two systems using the Mw 6.5 Norcia (Central
   Italy) earthquake that occurred on 30 October 2016 as an example of a
   well-recorded earthquake that triggered major interest in the
   seismological and earthquake engineering communities. The RRSM is a
   fully automated system for rapid dissemination of earthquake shaking
   information, whereas the ESM provides qualitychecked, manually processed
   waveforms and reviewed earthquake information. The RRSM uses only data
   from the European Integrated Waveform Data Archive, whereas the ESM also
   includes offline data from other sources, such as the ITalian
   ACcelerometric Archive (ITACA). Advanced software tools are also
   included in the ESM to allow users to process strong-motion data and to
   select ground-motion waveform sets for seismic structural analyses. The
   RRSM and ESM are complementary services designed fora variety of
   possible stakeholders, ranging from scientists to the educated general
   public. The RRSM and ESM are developed, organized, and reviewed by
   selected members of the seismological community in Europe, including
   strong-motion data providers and expert users. Global access and usage
   of the data is encouraged. The ESM is presently the reference database
   for harmonized seismic hazard and risk studies in Europe. ORFEUS
   strong-motion data are open, ?Findable, Accessible, Interoperable, and
   Reusable,? and accompanied by licensing information. The users are
   encouraged to properly cite the data providers, using the digital object
   identifiers of the seismic networks.},
Publisher = {SEISMOLOGICAL SOC AMER},
Address = {400 EVELYN AVE, SUITE 201, ALBANY, CA 94706-1375 USA},
Type = {Article},
Language = {English},
Affiliation = {Lanzano, G (Corresponding Author), Ist Nazl Geofis \& Vulcanol INGV, Milan, Italy.
   Lanzano, Giovanni; Luzi, Lucia; D'Amico, Maria; Felicetta, Chiara; Puglia, Rodolfo; Russo, Emiliano, Ist Nazl Geofis \& Vulcanol INGV, Milan, Italy.
   Cauzzi, Carlo, Swiss Fed Inst Technol, ORFEUS, Zurich, Switzerland.
   Cauzzi, Carlo; Clinton, John, Swiss Fed Inst Technol, Swiss Seismol Serv, Zurich, Switzerland.
   Bienkowski, Jarek; Sleeman, Reinoud, Koninklijk Nederlands Meteorol Inst KNMI, De Bilt, Netherlands.
   Bindi, Dino, German Res Ctr Geosci GFZ, Potsdam, Germany.
   Cocco, Massimo, EPOS ERIC, Rome, Italy.
   Cocco, Massimo; Lauciani, Valentino; Michelini, Alberto, Ist Nazl Geofis \& Vulcanol INGV, Rome, Italy.
   Douglas, John, Univ Strathclyde, Glasgow, Lanark, Scotland.
   Faenza, Licia, Ist Nazl Geofis \& Vulcanol INGV, Bologna, Italy.
   Gallovic, Frantisek, Charles Univ Prague, Dept Geophys, Prague, Czech Republic.
   Giardini, Domenico, Swiss Fed Inst Technol, Zurich, Switzerland.
   Ktenidou, Olga-Joan, Natl Observ Athens NOA, Inst Geodynam, Athens, Greece.
   Manakou, Maria, Aristotle Univ Thessaloniki AUTH, Thessaloniki, Greece.
   Marmureanu, Alexandru, Natl Inst Earth Phys NIEP, Magurele, Romania.
   Maufroy, Emeline, Univ Grenoble Alpes, Grenoble, France.
   Ozener, Haluk, Bogazici Univ, Kandilli Observ, Istanbul, Turkey.
   Ozener, Haluk, Bogazici Univ, Earthquake Res Inst KOERI, Istanbul, Turkey.
   Rupakhety, Rajesh, Univ Iceland, Reykjavik, Iceland.
   Shahvar, Mohammad, Rd Housing \& Urban Dev Res Ctr BHRC, Tehran, Iran.
   Theodoulidis, Nikolaos, Inst Engn Seismol \& Earthquake Engn ITSAK, Thessaloniki, Greece.},
DOI = {10.1785/0220200398},
ISSN = {0895-0695},
EISSN = {1938-2057},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {giovanni.lanzano@ingv.it},
Affiliations = {Istituto Nazionale Geofisica e Vulcanologia (INGV); Swiss Federal
   Institutes of Technology Domain; ETH Zurich; Swiss Federal Institutes of
   Technology Domain; ETH Zurich; Royal Netherlands Meteorological
   Institute; Helmholtz Association; Helmholtz-Center Potsdam GFZ German
   Research Center for Geosciences; Istituto Nazionale Geofisica e
   Vulcanologia (INGV); University of Strathclyde; Istituto Nazionale
   Geofisica e Vulcanologia (INGV); Charles University Prague; Swiss
   Federal Institutes of Technology Domain; ETH Zurich; National
   Observatory of Athens; Aristotle University of Thessaloniki; Communaute
   Universite Grenoble Alpes; Universite Grenoble Alpes (UGA); Bogazici
   University; Bogazici University; University of Iceland},
ResearcherID-Numbers = {Gallovic, Frantisek/G-7986-2011
   Lanzano, Giovanni/AAR-8264-2021
   Ozener, Haluk/A-1860-2016
   Marmureanu, Alexandru/C-5731-2012
   Lanzano, Giovanni/HKO-7234-2023
   Maufroy, Emeline/AGW-1207-2022
   D'Amico, Maria/A-1492-2019
   Cocco, Massimo/G-6872-2012
   Ktenidou, Olga-Joan/AAI-1465-2020
   Bindi, Dino/AAY-6768-2021
   Luzi, Lucia/AAC-7857-2020
   Douglas, John/A-3098-2011
   Cauzzi, Carlo/H-5641-2011
   },
ORCID-Numbers = {Gallovic, Frantisek/0000-0002-9268-3923
   Lanzano, Giovanni/0000-0001-7947-4281
   Ozener, Haluk/0000-0003-2531-3030
   Marmureanu, Alexandru/0000-0002-2181-4471
   Maufroy, Emeline/0000-0002-0995-5597
   D'Amico, Maria/0000-0002-1677-1294
   Cocco, Massimo/0000-0001-6798-4225
   Ktenidou, Olga-Joan/0000-0001-5206-5699
   Luzi, Lucia/0000-0003-4312-580X
   Douglas, John/0000-0003-3822-0060
   Sleeman, Reinoud/0000-0002-1928-5056
   Cauzzi, Carlo/0000-0003-2033-4537
   Lauciani, Valentino/0000-0002-9672-7428
   Clinton, John/0000-0001-8626-2703},
Funding-Acknowledgement = {Observatories and Research Facilities for European Seismology (ORFEUS)
   strong-motion program through the European Commission {[}GA 262330];
   Seismology and Earthquake Engineering Research Infrastructure Alliance
   for Europe (SERA) {[}GA 730900]; European Plate Observing System -
   Implementation Phase (EPOS-IP) within the framework of the EPOS Thematic
   Core Service for Seismology {[}676564]},
Funding-Text = {The Observatories and Research Facilities for European Seismology
   (ORFEUS) strong-motion program received partial support through the
   European Commission-funded projects: Network of European Research
   Infrastructures for Earthquake Risk Assessment and Mitigation (NERA; GA
   262330); Seismology and Earthquake Engineering Research Infrastructure
   Alliance for Europe (SERA; http://www.sera-eu.org/en/home/; GA 730900);
   and European Plate Observing System - Implementation Phase (EPOS-IP;
   https://eposip.org/; 676564) within the framework of the EPOS Thematic
   Core Service for Seismology. The authors are thankful to Florian
   Haslinger for coordinating EPOS Seismology during EPOS IP and beyond.
   The authors are thankful to the members of the ORFEUS Strong-Motion
   Service Management Committee
   (http://orfeus-eu.org/organization/structure/) and to the institutions
   (http://orfeus-eu.org/organization/corporate\_founders/;
   http://orfeus-eu.org/organization/participation/) and individuals who
   seamlessly and enthusiastically contribute to and improve ORFEUS
   initiatives.},
Number-of-Cited-References = {35},
Times-Cited = {9},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Seismol. Res. Lett.},
Doc-Delivery-Number = {RU0GE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000644829600002},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000608437800092,
Author = {Creasy, Heather Huot and Felix, Victor and Aluvathingal, Jain and
   Crabtree, Jonathan and Ifeonu, Olukemi and Matsumura, James and
   McCracken, Carrie and Nickel, Lance and Orvis, Joshua and Schor, Mike
   and Giglio, Michelle and Mahurkar, Anup and White, Owen},
Title = {HMPDACC: a Human Microbiome Project Multi-omic data resource},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2021},
Volume = {49},
Number = {D1},
Pages = {D734-D742},
Month = {JAN 8},
Abstract = {The Human Microbiome Project (HMP) explored microbial communities of the
   human body in both healthy and disease states. Two phases of the HMP
   (HMP and iHMP) together generated >48TB of data (public and controlled
   access) from multiple, varied omics studies of both the microbiome and
   associated hosts. The Human Microbiome Project Data Coordination Center
   (HMPDACC) was established to provide a portal to access data and
   resources produced by the HMP. The HMPDACC provides a unified data
   repository, multi-faceted search functionality, analysis pipelines and
   standardized protocols to facilitate community use of HMP data. Recent
   efforts have been put toward making HMP data more findable, accessible,
   interoperable and reusable. HMPDACC resources are freely available at
   www.hmpdacc.org.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Creasy, HH (Corresponding Author), Univ Maryland, Inst Genome Sci, Sch Med, Baltimore, MD 21201 USA.
   Creasy, Heather Huot; Felix, Victor; Aluvathingal, Jain; Crabtree, Jonathan; Ifeonu, Olukemi; Matsumura, James; McCracken, Carrie; Nickel, Lance; Orvis, Joshua; Schor, Mike; Giglio, Michelle; Mahurkar, Anup; White, Owen, Univ Maryland, Inst Genome Sci, Sch Med, Baltimore, MD 21201 USA.
   Matsumura, James, Dina, Chicago, IL 60602 USA.},
DOI = {10.1093/nar/gkaa996},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {DYNAMICS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {hhuot@som.umaryland.edu},
Affiliations = {University System of Maryland; University of Maryland Baltimore},
Funding-Acknowledgement = {National Institutes of Health {[}U01HG004866, U54HD080784, U54DK102557,
   U54DK102556, OT3OD025459]},
Funding-Text = {National Institutes of Health {[}U01HG004866, U54HD080784, U54DK102557,
   U54DK102556, OT3OD025459]. Funding for open access charge: National
   Institutes of Health {[}U54DK102556].},
Number-of-Cited-References = {22},
Times-Cited = {11},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {PT2GR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000608437800092},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000313611100012,
Author = {Lato, M. and Kemeny, J. and Harrap, R. M. and Bevan, G.},
Title = {Rock bench: Establishing a common repository and standards for assessing
   rockmass characteristics using LiDAR and photogrammetry},
Journal = {COMPUTERS \& GEOSCIENCES},
Year = {2013},
Volume = {50},
Number = {SI},
Pages = {106-114},
Month = {JAN},
Abstract = {Remote sensing methods are now used to assess rockmass characteristics
   along transportation corridors, in mines and tunnels, and in other areas
   where rock falls can affect humans and infrastructure. A variety of
   sensor methods, primarily LiDAR and photogrammetry, have seen recent use
   with widespread success and state of practice acceptance. Various
   commercial and custom tools exist to process the resulting data to
   extract geometry, surface and location based statistics, and to perform
   kinematic stability assessments. Although there is a widespread need to
   assess how different sensors and processing workflows actually perform,
   these are often compared anecdotally solely with the field practices
   they replace and using site and sensor data unavailable to other
   researchers.
   Two principles must be established to move across-the-board comparisons
   of remote rockmass characterization forward: (i) establishment of
   accessible, documented test sites, and (ii) test databases that are
   accessible to all. We propose the establishment of several key sites for
   equipment tests, including already-studied areas in Europe and North
   America, as well as an open approach to adding sites and related data to
   the collection. Site descriptions must include detailed local geology,
   photographs, LiDAR and/or photogrammetry datasets, and access notes.
   Second, we describe and provide a prototype data repository for storing
   this information, and in particular for providing open access to
   benchmark data into the future. This initiative will allow for
   meaningful comparisons of sensors and algorithms, and specifically will
   support better methodologies for benchmarking rock mass data in the
   geosciences. Data and metadata will be hosted at the www.rockbench.org
   domain. (C) 2012 Elsevier Ltd. All rights reserved.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Lato, M (Corresponding Author), Norwegian Geotech Inst, Oslo, Norway.
   Lato, M., Norwegian Geotech Inst, Oslo, Norway.
   Kemeny, J., Univ Arizona, Tucson, AZ 85721 USA.
   Harrap, R. M., Queens Univ, Kingston, ON K7L 3N6, Canada.},
DOI = {10.1016/j.cageo.2012.06.014},
ISSN = {0098-3004},
EISSN = {1873-7803},
Keywords = {Benchmarking; Engineering geology; LiDAR; Photogrammetry; Remote
   sensing; Rockfall},
Keywords-Plus = {DISCONTINUITY ORIENTATION},
Research-Areas = {Computer Science; Geology},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Geosciences,
   Multidisciplinary},
Author-Email = {mjlato@gmail.com},
Affiliations = {Norwegian Geotechnical Institute, NGI; University of Arizona; Queens
   University - Canada},
ORCID-Numbers = {Lato, Matt/0000-0002-4284-4899},
Funding-Acknowledgement = {Natural Science and Engineering Research Council of Canada; Norwegian
   Research Council},
Funding-Text = {This work publishes data collected by the authors as well as various
   engineers and scientists, including Michael Fergusson, Elin Morgan, and
   Heidi Haugland. The equipments used to collect the data are owned by
   Jean Hutchinson, Mark Diederichs, George Bevan, John Kemeny, and the
   Norwegian Geotechnical Institute. This work has been generously funded
   by the Natural Science and Engineering Research Council of Canada and
   the Norwegian Research Council.},
Number-of-Cited-References = {27},
Times-Cited = {67},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {74},
Journal-ISO = {Comput. Geosci.},
Doc-Delivery-Number = {071RE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000313611100012},
DA = {2024-01-15},
}

@article{ WOS:000708917900001,
Author = {Puttonen, Tuomas and Salmi, Mika and Partanen, Jouni},
Title = {Mechanical properties and fracture characterization of additive
   manufacturing polyamide 12 after accelerated weathering},
Journal = {POLYMER TESTING},
Year = {2021},
Volume = {104},
Month = {DEC},
Abstract = {The additive manufacturing (AM) methods, selective laser sintering (SLS)
   and multi jet fusion (MJF), are increasingly used for end-use polymer
   parts. Chemical reactions caused by ionizing radiation and catalyzed by
   oxygen, moisture, and heat are known to degrade the polymer structure,
   result in visual defects, and loss of mechanical properties. However,
   the effects of the AM layer-wise manufacturing process on polymer
   degradation are not widely studied. Yet, they may have implications on
   the mechanical properties and fracture mechanisms of the components.
   This paper presents an open access data repository of mechanical
   properties after weathering for AM plastics, conventionally manufactured
   plastics, and for two clear protective coatings. All materials were
   exposed to a 1500-h accelerated weathering cycle (ISO-4982-3) followed
   by tensile testing (ISO-527). Special attention was given to polyamide
   12 (PA12) produced via powder bed fusion AM in two build orientations.
   The fracture surfaces of PA12 and glass-filled PA12 were further studied
   with scanning electron microscopy. The AM materials were PA12,
   glass-filled PA12, and carbon reinforced PA12. Traditionally
   manufactured materials included glass-filled and molybdenum
   disulfide-filled PA66, PMMA, ABS, PC, and cast PA12.
   No clear differences were found between the AM build orientations in
   fracture mechanisms or weathering performance. AM and cast PA12 were
   strongly affected by accelerated weathering. Carbon reinforced PA12 with
   a UV varnish experienced the least changes. Weathering resistance was
   increased with protective coatings. However, an increase in the
   deviation of mechanical properties with the coatings was observed. The
   contrary results in ductility for the glass-filled and molybdenum
   disulfide-filled PA66 after weathering would merit further studies.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Puttonen, T (Corresponding Author), Aalto Univ, Dept Mech Engn Otakaari 4, Sch Engn, Espoo 02150, Finland.
   Puttonen, Tuomas; Salmi, Mika; Partanen, Jouni, Aalto Univ, Dept Mech Engn Otakaari 4, Sch Engn, Espoo 02150, Finland.},
DOI = {10.1016/j.polymertesting.2021.107376},
EarlyAccessDate = {OCT 2021},
Article-Number = {107376},
ISSN = {0142-9418},
EISSN = {1873-2348},
Keywords = {Additive manufacturing; Powder bed fusion; Accelerated weathering;
   Polymer degradation; Mechanical properties; Fracture characterization},
Keywords-Plus = {MULTI JET FUSION; ALIPHATIC POLYAMIDES; DEGRADATION; POLYMERS;
   PHOTOOXIDATION; PERFORMANCE; BEHAVIOR; PHOTOCHEMISTRY; MICROSTRUCTURE;
   EMBRITTLEMENT},
Research-Areas = {Materials Science; Polymer Science},
Web-of-Science-Categories  = {Materials Science, Characterization \& Testing; Polymer Science},
Author-Email = {tuomas.puttonen@aalto.fi
   mika.salmi@aalto.fi
   jouni.partanen@aalto.fi},
Affiliations = {Aalto University},
ResearcherID-Numbers = {Partanen, Jouni P/K-4291-2013
   Salmi, Mika/E-7216-2012
   },
ORCID-Numbers = {Salmi, Mika/0000-0002-7295-3551
   Puttonen, Tuomas/0000-0003-0168-8962},
Funding-Acknowledgement = {Technical Research Institute of Finland (VTT) {[}632/31/2018]; Aalto
   University (Foundation) {[}632/31/2018]},
Funding-Text = {This research was done and funded as part of a Business Finland project
   DIVALIITO (632/31/2018) between the Aalto University (Foundation), the
   Technical Research Institute of Finland (VTT), and participating
   consortium companies.},
Number-of-Cited-References = {69},
Times-Cited = {15},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {38},
Journal-ISO = {Polym. Test},
Doc-Delivery-Number = {WJ2ZV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000708917900001},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000832309800001,
Author = {Ozigbu, Chamberline E. and Olatosi, Bankole and Li, Zhenlong and Hardin,
   James W. and Hair, Nicole L.},
Title = {Correlates of Zero-Dose Vaccination Status among Children Aged 12-59
   Months in Sub-Saharan Africa: A Multilevel Analysis of Individual and
   Contextual Factors},
Journal = {VACCINES},
Year = {2022},
Volume = {10},
Number = {7},
Month = {JUL},
Abstract = {Despite ongoing efforts to improve childhood vaccination coverage,
   including in hard-to-reach and hard-to-vaccinate communities, many
   children in sub-Saharan Africa (SSA) remain unvaccinated. Considering
   recent goals set by the Immunization Agenda 2030 (IA2030), including
   reducing the number of zero-dose children by half, research that goes
   beyond coverage to identify populations and groups at greater risk of
   being unvaccinated is urgently needed. This is a pooled cross-sectional
   study of individual- and country-level data obtained from Demographic
   and Health Surveys Program and two open data repositories. The sample
   includes 43,131 children aged 12-59 months sampled between 2010 and 2020
   in 33 SSA countries. Associations of zero-dose status with individual
   and contextual factors were assessed using multilevel logistic
   regression. 16.5\% of children had not received any vaccines. Individual
   level factors associated lower odds of zero-dose status included
   mother's primary school or high school education, employment, use of
   antenatal care services and household wealth. Compared to children in
   countries with lower GDP, children in countries with relatively high GDP
   had nearly four times greater odds of being unvaccinated. Both
   individual and contextual factors are correlated with zero-dose status
   in SSA. Our results can inform efforts to identify and reach children
   who have not received any vaccines.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Hair, NL (Corresponding Author), Univ South Carolina, Dept Hlth Serv Policy \& Management, Arnold Sch Publ Hlth, Columbia, SC 29208 USA.
   Ozigbu, Chamberline E.; Olatosi, Bankole; Hardin, James W.; Hair, Nicole L., Univ South Carolina, Dept Hlth Serv Policy \& Management, Arnold Sch Publ Hlth, Columbia, SC 29208 USA.
   Olatosi, Bankole; Li, Zhenlong, Univ South Carolina, South Carolina SmartState Ctr Hlthcare Quality, Arnold Sch Publ Hlth, Columbia, SC 29208 USA.
   Olatosi, Bankole; Li, Zhenlong, Univ South Carolina, Big Data Hlth Sci Ctr BDHSC, Columbia, SC 29208 USA.
   Li, Zhenlong, Univ South Carolina, Geoinformat \& Big Data Res Lab, Columbia, SC 29208 USA.
   Hardin, James W., Univ South Carolina, Arnold Sch Publ Hlth, Dept Epidemiol \& Biostat, Columbia, SC 29208 USA.},
DOI = {10.3390/vaccines10071052},
Article-Number = {1052},
EISSN = {2076-393X},
Keywords = {infectious diseases; vaccination; immunization; zero-dose; children;
   sub-Saharan Africa},
Keywords-Plus = {BRIEF CONCEPTUAL TUTORIAL; BIRTH-WEIGHT INFANTS; LOGISTIC-REGRESSION;
   SOCIAL EPIDEMIOLOGY; MATERNAL EDUCATION; IMMUNIZATION COVERAGE;
   INCREASING COVERAGE; POLIO ERADICATION; HEALTH; COMMUNITY},
Research-Areas = {Immunology; Research \& Experimental Medicine},
Web-of-Science-Categories  = {Immunology; Medicine, Research \& Experimental},
Author-Email = {cozigbu@email.sc.edu
   olatosi@mailbox.sc.edu
   zhenlong@mailbox.sc.edu
   jhardin@mailbox.sc.edu
   hairnl@mailbox.sc.edu},
Affiliations = {University of South Carolina System; University of South Carolina
   Columbia; University of South Carolina System; University of South
   Carolina Columbia; University of South Carolina System; University of
   South Carolina Columbia; University of South Carolina System; University
   of South Carolina Columbia; University of South Carolina System;
   University of South Carolina Columbia},
ResearcherID-Numbers = {Li, Zhenlong/M-1065-2017
   Hardin, James William/Q-7617-2016
   Hair, Nicole/HJG-7091-2022
   Hardin, James William/P-4772-2019},
ORCID-Numbers = {Li, Zhenlong/0000-0002-8938-5466
   Hardin, James William/0000-0003-0506-5500
   Hair, Nicole/0000-0001-8559-5717
   Hardin, James William/0000-0003-0506-5500},
Funding-Acknowledgement = {SPARC Graduate Research Grant from the Office of the Vice President for
   Research at the University of South Carolina},
Funding-Text = {This work was partially supported by a SPARC Graduate Research Grant
   from the Office of the Vice President for Research at the University of
   South Carolina.},
Number-of-Cited-References = {73},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Vaccines},
Doc-Delivery-Number = {3H8WB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000832309800001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000361047200001,
Author = {Wan, Quan and Dingerdissen, Hayley and Fan, Yu and Gulzar, Naila and
   Pan, Yang and Wu, Tsung-Jung and Yan, Cheng and Zhang, Haichen and
   Mazumder, Raja},
Title = {BioXpress: an integrated RNA-seq-derived gene expression database for
   pan-cancer analysis},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2015},
Month = {MAR 28},
Abstract = {BioXpress is a gene expression and cancer association database in which
   the expression levels are mapped to genes using RNA-seq data obtained
   from The Cancer Genome Atlas, International Cancer Genome Consortium,
   Expression Atlas and publications. The BioXpress database includes
   expression data from 64 cancer types, 6361 patients and 17 469 genes
   with 9513 of the genes displaying differential expression between tumor
   and normal samples. In addition to data directly retrieved from RNA-seq
   data repositories, manual biocuration of publications supplements the
   available cancer association annotations in the database. All cancer
   types are mapped to Disease Ontology terms to facilitate a uniform
   pan-cancer analysis. The BioXpress database is easily searched using
   HUGO Gene Nomenclature Committee gene symbol, UniProtKB/RefSeq accession
   or, alternatively, can be queried by cancer type with specified
   significance filters. This interface along with availability of
   pre-computed downloadable files containing differentially expressed
   genes in multiple cancers enables straightforward retrieval and display
   of a broad set of cancer-related genes.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Mazumder, R (Corresponding Author), George Washington Univ, Dept Biochem \& Mol Med, Washington, DC 20037 USA.
   Wan, Quan; Dingerdissen, Hayley; Fan, Yu; Gulzar, Naila; Pan, Yang; Wu, Tsung-Jung; Yan, Cheng; Zhang, Haichen; Mazumder, Raja, George Washington Univ, Dept Biochem \& Mol Med, Washington, DC 20037 USA.
   Mazumder, Raja, George Washington Univ, McCormick Genom \& Prote Ctr, Washington, DC 20037 USA.},
DOI = {10.1093/database/bav019},
Article-Number = {bav019},
ISSN = {1758-0463},
Keywords-Plus = {MATRIX METALLOPROTEINASES; MOLECULAR CLASSIFICATION; MT1G
   HYPERMETHYLATION; MICROCEPHALY GENES; IDENTIFICATION; METASTASIS;
   INVASION; BIOLOGY; TISSUES; HE-4},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {mazumder@gwu.edu},
Affiliations = {George Washington University; George Washington University},
ResearcherID-Numbers = {Yan, C/K-5830-2019
   Pan, Yang/CAH-7969-2022
   Zhang, Haichen/AAI-2096-2019
   Pan, Yang/CAF-2170-2022
   Pan, Yang/IAO-4486-2023
   },
ORCID-Numbers = {Pan, Yang/0000-0003-3487-7233
   Zhang, Haichen/0000-0002-0615-2836
   Pan, Yang/0000-0003-3487-7233
   Pan, Yang/0000-0003-3487-7233
   Mazumder, Raja/0000-0001-8823-9945
   GULZAR, NAILA/0000-0002-8138-8312},
Funding-Acknowledgement = {NCI/EDRN {[}156620]; RM research funds},
Funding-Text = {This project was partially funded by NCI/EDRN Associate Member contract
   \#156620. Funding open access charge: RM research funds.},
Number-of-Cited-References = {88},
Times-Cited = {62},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {14},
Journal-ISO = {Database},
Doc-Delivery-Number = {CR0XO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000361047200001},
OA = {Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000467182100001,
Author = {Meresh, Edwin S. and Artin, Hewa and Joyce, Cara and Birch, Steven and
   Daniels, David and Owens, Jack H. and La Rosa, Alvaro J. and Rao, Murali
   S. and Halaris, Angelos},
Title = {Obstructive sleep apnea co-morbidity in patients with fibromyalgia: a
   single-center retrospective analysis and literature review},
Journal = {OPEN ACCESS RHEUMATOLOGY-RESEARCH AND REVIEWS},
Year = {2019},
Volume = {11},
Pages = {103-109},
Abstract = {Background: Fibromyalgia (FM) is a chronic medical condition
   characterized by widespread pain, sleep disturbance, and cognitive
   dysfunction. Sleep disorders are thought to play a prominent role in the
   etiology and symptomatic management of FM, specifically obstructive
   sleep apnea (OSA). In order to provide collaborative care, we need a
   better understanding of any overlapping presentation of FM and OSA. We
   conducted a site-wide review of patients from 2012-2016 to identify FM
   patients diagnosed with OSA.
   Methods: Charts were reviewed in patients aged 18 and above from
   2012-2016 using ICD codes from a clinical data repository. Intersection
   of patients with a diagnosis of FM and OSA in clinics of psychiatry,
   sleep, rheumatology, and other outpatient clinics was compared.
   Polysomnography order patterns for FM patients were investigated.
   Results: Co-morbidity was highest in the sleep clinic (85.8\%) compared
   to psychiatry (42.0\%), rheumatology (18.7\%), and other outpatient
   clinics (3.6\%) (p<0.001). In the rheumatology and other outpatient
   clinics, 93.5\% and 96\% of patients respectively, had no
   polysomnography ordered. Pairwise comparison of co-morbidity in clinics:
   sleep vs psychiatry, sleep vs rheumatology, sleep vs other clinics,
   psychiatry vs rheumatology, psychiatry vs other clinics, and
   rheumatology vs other clinics were statistically significant after
   applying a Sidak adjustment to the p-values (all p<0.001).
   Conclusion: Our analysis suggests that there could be a correlation
   between FM and OSA, and referral to sleep studies is recommended in the
   management of patients with FM. The varying prevalence of FM patients
   with co-morbid OSA in sleep clinics when compared to other outpatient
   clinics suggests a discrepancy in the identification of FM patients with
   OSA. When properly screened, OSA co-morbidity has the potential to be
   higher in other outpatient clinics.},
Publisher = {DOVE MEDICAL PRESS LTD},
Address = {PO BOX 300-008, ALBANY, AUCKLAND 0752, NEW ZEALAND},
Type = {Review},
Language = {English},
Affiliation = {Meresh, ES (Corresponding Author), Loyola Univ Med Ctr, Dept Psychiat, 2160 S First Ave,Bldg 105,Rm 1940, Maywood, IL 60153 USA.
   Meresh, Edwin S.; Daniels, David; Owens, Jack H.; La Rosa, Alvaro J.; Rao, Murali S.; Halaris, Angelos, Loyola Univ Med Ctr, Dept Psychiat, 2160 S First Ave,Bldg 105,Rm 1940, Maywood, IL 60153 USA.
   Artin, Hewa, Loyola Stritch Sch Med, Maywood, IL 60153 USA.
   Joyce, Cara, Loyola Univ Med Ctr, Biostat Core, Clin Res Off, Maywood, IL 60153 USA.
   Birch, Steven, Loyola Univ Med Ctr, Informat \& Syst Dev, Maywood, IL 60153 USA.},
DOI = {10.2147/OARRR.S196576},
ISSN = {1179-156X},
Keywords = {fibromyalgia; obstructive sleep apnea; co-morbidity; sleep;
   rheumatology; psychiatry},
Keywords-Plus = {HEALTH-CARE UTILIZATION; QUALITY-OF-LIFE; ECONOMIC BURDEN;
   CHRONIC-FATIGUE; PAIN; ASSOCIATION; PATTERNS; DISORDER; WOMEN},
Research-Areas = {Rheumatology},
Web-of-Science-Categories  = {Rheumatology},
Author-Email = {Emeresh@lumc.edu},
Affiliations = {Loyola University Chicago; Loyola University Chicago; Loyola University
   Chicago; Loyola University Chicago},
ResearcherID-Numbers = {Joyce, Cara/Z-2075-2018
   },
ORCID-Numbers = {Joyce, Cara/0000-0003-0468-8271
   Birch, Steven/0000-0001-8610-7690
   Meresh, Edwin/0000-0002-8278-9601},
Number-of-Cited-References = {36},
Times-Cited = {9},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Open Access Rehumatol.},
Doc-Delivery-Number = {HX1VV},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000467182100001},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000548092600001,
Author = {Liew, Hui-Peng and Eidem, Nathan},
Title = {Assessing the spatial-temporal clustering and health implications of
   fine particulate matter (PM2.5)},
Journal = {JOURNAL OF PUBLIC HEALTH-HEIDELBERG},
Year = {2022},
Volume = {30},
Number = {4},
Pages = {789-799},
Month = {APR},
Abstract = {Aim This study seeks to examine changes in the mean annual exposure of
   PM2.5 air pollution from 1990 to 2000 and how they are associated with
   change in mortality due to tuberculosis, trachea/bronchus/lung cancer,
   respiratory diseases, and cardiovascular diseases from 2000 to 2016. A
   secondary goal of this study is to use spatial-temporal clustering to
   examine how PM2.5 trends differ across countries. Methods The empirical
   work of this study is based on the World Bank Open Data and the World
   Health Organization's Global Health Observatory (GHO) Data Repository.
   Quantile regression and spatial-temporal cluster analysis are used to
   assess the aims of this study. Results Findings from the quantile
   regression revealed that the number of deaths associated with these
   diseases differ according to the different levels of changes in PM2.5
   concentration. Findings also reveal that countries assigned to different
   clusters are markedly different in terms of PM2.5 trends. Findings imply
   that air pollution inequality should be considered a factor in the
   elimination of health inequality. Conclusion Efforts to integrate
   disease surveillance and control programs with those that reduce
   exposure to fine particulate matter, improve air quality, and increase
   people's awareness of the health implications of air pollution should be
   continued or encouraged.},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Liew, HP (Corresponding Author), Univ Nebraska Kearney, Dept Sociol, Copeland Hall 120, Kearney, NE 68849 USA.
   Liew, Hui-Peng, Univ Nebraska Kearney, Dept Sociol, Copeland Hall 120, Kearney, NE 68849 USA.
   Eidem, Nathan, Univ Nebraska Kearney, Dept Geog, Copeland Hall 203, Kearney, NE 68849 USA.},
DOI = {10.1007/s10389-020-01346-4},
EarlyAccessDate = {JUL 2020},
ISSN = {2198-1833},
EISSN = {1613-2238},
Keywords = {Fine particulate matter; PM2; 5; Air pollution; Quantile regression;
   Spatial-temporal clustering},
Keywords-Plus = {AIR-POLLUTION; DISEASE; TUBERCULOSIS; ASSOCIATION; MORTALITY; EXPOSURE;
   IMPACT},
Research-Areas = {Public, Environmental \& Occupational Health},
Web-of-Science-Categories  = {Public, Environmental \& Occupational Health},
Author-Email = {liewhp@tmk.edu},
Affiliations = {University of Nebraska System; University Nebraska Kearney; University
   of Nebraska System; University Nebraska Kearney},
Number-of-Cited-References = {20},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {15},
Journal-ISO = {J. Public Health-Heidelberg},
Doc-Delivery-Number = {ZV1TJ},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000548092600001},
DA = {2024-01-15},
}

@article{ WOS:000708726500002,
Author = {Hayes, Kyle and Panaccio, Mary P. and Houston, Parul and Niewoehner,
   John and Fahim, Mohammed and Wan, George J. and Dhillon, Bhavna},
Title = {Real-World Treatment Patterns and Outcomes from an Electronic Medical
   Records Database for Patients with Rheumatoid Arthritis Treated with
   Repository Corticotropin Injection},
Journal = {OPEN ACCESS RHEUMATOLOGY-RESEARCH AND REVIEWS},
Year = {2021},
Volume = {13},
Pages = {315-323},
Abstract = {Purpose: Repository corticotropin injection (RCI; Acthar (R) Gel) is a
   naturally sourced mixture of adrenocorticotropic hormone analogs and
   other pituitary peptides that exerts anti-inflammatory and
   immunomodulatory properties via melanocortin receptors. RCI is approved
   as a short-term adjunctive therapy for rheumatoid arthritis (RA) and is
   typically used in patients with refractory RA. The objective of this
   study was to describe real-world outcomes of RA patients treated with
   RCI by retrospective analysis of an electronic medical records (EMR)
   database.
   Patients and Methods: EMR data were obtained from the United
   Rheumatology-Normal Integrated Community Evidence (UR-NICE (TM)) data
   repository for patients who used RCI for the treatment of RA.
   Demographics, comorbidities, disease history, medications, and
   laboratory evaluations 365 days prior to and 365 days after initiation
   of RCI were examined.
   Results: The patient cohort was predominantly White females with a mean
   age of 60 years and high RA activity prior to RCI therapy. Clinical
   measures of disease severity indicated that patients had high RA
   activity before starting RCI therapy. Clinical Disease Activity Index
   (CDAI) scores were significantly reduced 365 days post-initiation of
   RCI. Swollen and tender joint counts and patient-reported outcomes,
   including Routine Assessment of Patient Index Data 3 (RAPID3), Physician
   Global Assessment, and patient assessment of pain severity were also
   significantly lower. The number of patients taking conventional
   synthetic (cs) disease-modifying antirheumatic drugs (DMARDs), biologic
   (b) DMARDs, nonsteroidal anti-inflammatory drugs (NSAIDS), and opioids
   decreased, as did the number of drugs tried within each class for
   csDMARDs, bDMARDs, NSAIDs, and glucocorticoids.
   Conclusions: These findings suggest that RCI significantly improves
   clinical outcomes of RA and decreases the need for concomitant
   medications for up to 1 year following initiation of therapy. The study
   provides valuable insights into the use of RCI and management of these
   difficult-to-treat RA patients during routine clinical practice.},
Publisher = {DOVE MEDICAL PRESS LTD},
Address = {PO BOX 300-008, ALBANY, AUCKLAND 0752, NEW ZEALAND},
Type = {Article},
Language = {English},
Affiliation = {Hayes, K (Corresponding Author), Mallinckrodt Pharmaceut, Hampton, NJ 08827 USA.
   Hayes, Kyle; Panaccio, Mary P.; Houston, Parul; Niewoehner, John; Wan, George J., Mallinckrodt Pharmaceut, Hampton, NJ 08827 USA.
   Fahim, Mohammed, KMK Consulting, Morristown, NJ USA.
   Dhillon, Bhavna, United Rheumatol, Hauppauge, NY USA.},
DOI = {10.2147/OARRR.S329766},
ISSN = {1179-156X},
Keywords = {Acthar Gel; DMARDs; real-world evidence; rheumatoid arthritis;
   repository corticotropin injection; RCI; United Rheumatology database},
Keywords-Plus = {DISEASE-ACTIVITY SCORE; ACTIVITY INDEX CDAI; ROUTINE ASSESSMENT; RAPID3},
Research-Areas = {Rheumatology},
Web-of-Science-Categories  = {Rheumatology},
Author-Email = {kyle.hayes@mnk.com},
ResearcherID-Numbers = {Panaccio, Mary/HTT-4920-2023},
Funding-Acknowledgement = {Mallinckrodt Pharmaceuticals},
Funding-Text = {Professional writing and editorial support were provided by MedLogix
   Communications, LLC, Itasca, Illinois, under the direction of the
   authors and were funded by Mallinckrodt Pharmaceuticals. We thank
   Sung-Woo Ahn for assistance with data analysis.},
Number-of-Cited-References = {34},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Open Access Rehumatol.},
Doc-Delivery-Number = {WJ0FK},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000708726500002},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000362510300058,
Author = {Adams, Justin W. and Olah, Angela and McCurry, Matthew R. and Potze,
   Stephany},
Title = {Surface Model and Tomographic Archive of Fossil Primate and Other Mammal
   Holotype and Paratype Specimens of the Ditsong National Museum of
   Natural History, Pretoria, South Africa},
Journal = {PLOS ONE},
Year = {2015},
Volume = {10},
Number = {10},
Month = {OCT 6},
Abstract = {Nearly a century of paleontological excavation and analysis from the
   cave deposits of the Cradle of Humankind UNESCO World Heritage Site in
   northeastern South Africa underlies much of our understanding of the
   evolutionary history of hominins, other primates and other mammal
   lineages in the late Pliocene and early Pleistocene of Africa. As one of
   few designated fossil repositories, the Plio-Pleistocene Palaeontology
   Section of the Ditsong National Museum of Natural History (DNMNH; the
   former Transvaal Museum) curates much of the mammalian faunas recovered
   from the fossil-rich deposits of major South African hominin-bearing
   localities, including the holotype and paratype specimens of many
   primate, carnivore, and other mammal species (Orders Primates,
   Carnivora, Artiodactyla, Eulipotyphla, Hyracoidea, Lagomorpha,
   Perissodactyla, and Proboscidea). Here we describe an open-access
   digital archive of high-resolution, full-color three-dimensional (3D)
   surface meshes of all 89 non-hominin holotype, paratype and significant
   mammalian specimens curated in the Plio-Pleistocene Section vault.
   Surface meshes were generated using a commercial surface scanner (Artec
   Spider, Artec Group, Luxembourg), are provided in formats that can be
   opened in both open-source and commercial software, and can be readily
   downloaded either via an online data repository (MorphoSource) or via
   direct request from the DNMNH. In addition to providing surface meshes
   for each specimen, we also provide tomographic data (both computerized
   tomography {[}CT] and microfocus {[}microCT]) for a subset of these
   fossil specimens. This archive of the DNMNH Plio-Pleistocene collections
   represents the first research-quality 3D datasets of African mammal
   fossils to be made openly available. This simultaneously provides the
   paleontological community with essential baseline information (e.g.,
   updated listing and 3D record of specimens in their current state of
   preservation) and serves as a single resource of high-resolution digital
   data that improves},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Adams, JW (Corresponding Author), Monash Univ, Dept Anat \& Dev Biol, Fac Med Nursing \& Hlth Sci, Clayton, Vic, Australia.
   Adams, Justin W.; McCurry, Matthew R., Monash Univ, Dept Anat \& Dev Biol, Fac Med Nursing \& Hlth Sci, Clayton, Vic, Australia.
   Olah, Angela, Monash Univ, Fac Sci, Dept Biol Sci, Clayton, Vic, Australia.
   Olah, Angela; McCurry, Matthew R., Museum Victoria, Geosci, Carlton, Vic, Australia.
   Potze, Stephany, Ditsong Natl Museum Nat Hist, Dept Vertebrates, Pliopleistocene Palaeontol Sect, Pretoria, South Africa.},
DOI = {10.1371/journal.pone.0139800},
Article-Number = {e0139800},
ISSN = {1932-6203},
Keywords-Plus = {GEOMETRIC MORPHOMETRIC-ANALYSIS; RESOLUTION COMPUTED-TOMOGRAPHY;
   ENDOCRANIAL CAPACITY; DENTAL DEVELOPMENT; BONY LABYRINTH; TEMPORAL BONE;
   DIVERSITY; EVOLUTION; CRANIUM; SYSTEM},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {justin.adams@monash.edu},
Affiliations = {Monash University; Monash University; Museum Victoria},
ORCID-Numbers = {Adams, Justin/0000-0002-6214-9850
   McCurry, Matthew/0000-0002-2452-1404},
Funding-Acknowledgement = {Grand Valley State University through the GVSU Faculty Research
   Grant-in-Aid program; Department of Anatomy and Developmental Biology,
   Monash University},
Funding-Text = {Funding for the Artec Spider scanner used in this project was provided
   through internal funds made available to JWA by the Department of
   Anatomy and Developmental Biology, Monash University. Additional
   financial support for the acquisition of the suid CT datasets was
   provided by Grand Valley State University to JWA in 2006 through the
   GVSU Faculty Research Grant-in-Aid program. The funders had no role in
   study design, data collection and analysis, decision to publish, or
   preparation of the manuscript.},
Number-of-Cited-References = {94},
Times-Cited = {35},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {CT0TP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000362510300058},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000330911400013,
Author = {Campbell, Matthew P. and Nguyen-Khuong, Terry and Hayes, Catherine A.
   and Flowers, Sarah A. and Alagesan, Kathirvel and Kolarich, Daniel and
   Packer, Nicolle H. and Karlsson, Niclas G.},
Title = {Validation of the curation pipeline of UniCarb-DB: Building a global
   glycan reference MS/MS repository},
Journal = {BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS},
Year = {2014},
Volume = {1844},
Number = {1, A, SI},
Pages = {108-116},
Month = {JAN},
Abstract = {The UniCarb-DB database is an emerging public glycomics data repository,
   containing over 500 tandem mass spectra (as of March 2013) of glycans
   released from glycoproteins. A major challenge in glycomics research is
   to provide and maintain high-quality datasets that will offer the
   necessary diversity to support the development of accurate
   bioinformatics tools for data deposition and analySis. The role of
   UniCarb-DB, as an archival database, is to provide the glycomics
   community with open-access to a comprehensive LC MS/MS library of N- and
   O- linked glycans released from glycoproteins that have been annotated
   with glycosidic and cross-ring fragmentation ions, retention times, and
   associated experimental metadata descriptions. Here, we introduce the
   UniCarb-DB data submission pipeline and its practical application to
   construct a library of LC MS/MS glycan standards that forms part of this
   database. In this context, an independent consortium of three
   laboratories was established to analyze the same 23 commercially
   available oligosaccharide standards, all by using graphitized
   carbon-liquid chromatography (LC) electrospray ionization (ESI) ion trap
   mass spectrometry in the negative ion mode. A dot product score was
   calculated for each spectrum in the three sets of data as a measure of
   the comparability that is necessary for use of such a collection in
   library-based spectral matching and glycan structural identification.
   The effects of charge state, de-isotoping and threshold levels on the
   quality of the input data are shown. The provision of well-characterized
   oligosaccharide fragmentation data provides the opportunity to identify
   determinants of specific glycan structures, and will contribute to the
   confidence level of algorithms that assign glycan structures to
   experimental MS/MS spectra. This article is part of a Special Issue
   entitled: Computational Proteomics in the Post-Identification Era. Guest
   Editors: Martin Eisenacher and Christian Stephan. (C) 2013 Elsevier B.V.
   All rights reserved.},
Publisher = {ELSEVIER SCIENCE BV},
Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Packer, NH (Corresponding Author), Macquarie Univ, Sydney, NSW 2109, Australia.
   Campbell, Matthew P.; Nguyen-Khuong, Terry; Packer, Nicolle H., Macquarie Univ, Biomol Frontiers Res Ctr, Sydney, NSW 2109, Australia.
   Hayes, Catherine A.; Flowers, Sarah A.; Karlsson, Niclas G., Univ Gothenburg, Dept Med Biochem, Gothenburg, Sweden.
   Alagesan, Kathirvel; Kolarich, Daniel, Max Planck Inst Colloids \& Interfaces, Dept Biomol Syst, Potsdam, Germany.},
DOI = {10.1016/j.bbapap.2013.04.018},
ISSN = {1570-9639},
EISSN = {0006-3002},
Keywords = {Glycomics; Mass spectrometry; Database; Glycan; Standards; Glycobiology},
Keywords-Plus = {N-LINKED GLYCANS; TANDEM MASS-SPECTROMETRY; IMMUNE-SYSTEM; GLYCOMICS;
   TOOL; OLIGOSACCHARIDE; GLYCOSYLATION; SPECTRA; GLYCOPROTEINS; ANNOTATION},
Research-Areas = {Biochemistry \& Molecular Biology; Biophysics},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology; Biophysics},
Author-Email = {nicki.packer@mq.edu.au},
Affiliations = {Macquarie University; University of Gothenburg; Max Planck Society},
ResearcherID-Numbers = {Packer, Nicolle/Q-8929-2019
   Kolarich, Daniel/B-6893-2012
   Kolarich, Daniel/AAJ-3550-2020
   Karlsson, Niclas/G-5235-2013
   Hayes, Catherine/B-8973-2013
   Campbell, Matthew/D-8874-2015
   },
ORCID-Numbers = {Kolarich, Daniel/0000-0002-8452-1350
   Kolarich, Daniel/0000-0002-8452-1350
   Karlsson, Niclas/0000-0002-3045-2628
   Hayes, Catherine/0000-0002-3640-3237
   Packer, Nicolle/0000-0002-7532-4021
   Alagesan, Kathirvel/0000-0002-7596-5558
   Campbell, Matthew/0000-0002-9525-792X
   Flowers, Sarah/0000-0002-3513-2260},
Funding-Acknowledgement = {Max Planck Society; Bruker Daltonics and Agilent Technologies},
Funding-Text = {The authors thank Dextra Laboratories Ltd, UK, for the provision of the
   oligosaccharide standards. Many of the features described in this
   manuscript is built on the success of EUROCarbDB and we acknowledge all
   those involved for their on-going support. We also would like to thank
   the Max Planck Society, Bruker Daltonics and Agilent Technologies for
   their support.},
Number-of-Cited-References = {36},
Times-Cited = {47},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {26},
Journal-ISO = {BBA-Proteins Proteomics},
Doc-Delivery-Number = {AA2FV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000330911400013},
DA = {2024-01-15},
}

@article{ WOS:000760587900001,
Author = {Parsons, Miles J. G. and Lin, Tzu-Hao and Mooney, T. Aran and Erbe,
   Christine and Juanes, Francis and Lammers, Marc and Li, Songhai and
   Linke, Simon and Looby, Audrey and Nedelec, Sophie L. and Van Opzeeland,
   Ilse and Radford, Craig and Rice, Aaron N. and Sayigh, Laela and
   Stanley, Jenni and Urban, Edward and Di Iorio, Lucia},
Title = {Sounding the Call for a Global Library of Underwater Biological Sounds},
Journal = {FRONTIERS IN ECOLOGY AND EVOLUTION},
Year = {2022},
Volume = {10},
Month = {FEB 8},
Abstract = {Aquatic environments encompass the world's most extensive habitats, rich
   with sounds produced by a diversity of animals. Passive acoustic
   monitoring (PAM) is an increasingly accessible remote sensing technology
   that uses hydrophones to listen to the underwater world and represents
   an unprecedented, non-invasive method to monitor underwater
   environments. This information can assist in the delineation of
   biologically important areas via detection of sound-producing species or
   characterization of ecosystem type and condition, inferred from the
   acoustic properties of the local soundscape. At a time when worldwide
   biodiversity is in significant decline and underwater soundscapes are
   being altered as a result of anthropogenic impacts, there is a need to
   document, quantify, and understand biotic sound sources-potentially
   before they disappear. A significant step toward these goals is the
   development of a web-based, open-access platform that provides: (1) a
   reference library of known and unknown biological sound sources (by
   integrating and expanding existing libraries around the world); (2) a
   data repository portal for annotated and unannotated audio recordings of
   single sources and of soundscapes; (3) a training platform for
   artificial intelligence algorithms for signal detection and
   classification; and (4) a citizen science-based application for public
   users. Although individually, these resources are often met on regional
   and taxa-specific scales, many are not sustained and, collectively, an
   enduring global database with an integrated platform has not been
   realized. We discuss the benefits such a program can provide, previous
   calls for global data-sharing and reference libraries, and the
   challenges that need to be overcome to bring together bio- and
   ecoacousticians, bioinformaticians, propagation experts, web engineers,
   and signal processing specialists (e.g., artificial intelligence) with
   the necessary support and funding to build a sustainable and scalable
   platform that could address the needs of all contributors and
   stakeholders into the future.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Parsons, MJG (Corresponding Author), Australian Inst Marine Sci, Perth, WA, Australia.
   Parsons, Miles J. G., Australian Inst Marine Sci, Perth, WA, Australia.
   Lin, Tzu-Hao, Acad Sinica, Biodivers Res Ctr, Taipei, Taiwan.
   Mooney, T. Aran; Sayigh, Laela, Woods Hole Oceanog Inst, Dept Biol, Woods Hole, MA 02543 USA.
   Erbe, Christine, Curtin Univ, Ctr Marine Sci \& Technol, Perth, WA, Australia.
   Juanes, Francis, Univ Victoria, Dept Biol, Victoria, BC, Canada.
   Lammers, Marc, Hawaiian Isl Humpback Whale Natl Marine Sanctuary, Kihei, HI USA.
   Li, Songhai, Chinese Acad Sci, Marine Mammal \& Marine Bioacoust Lab, Inst Deep Sea Sci \& Engn, Sanya, Peoples R China.
   Linke, Simon, CSIRO, Dutton Pk, Qld, Australia.
   Looby, Audrey, Univ Florida, Fisheries \& Aquat Sci, Gainesville, FL USA.
   Looby, Audrey, Univ Florida, Inst Food \& Agr Sci UF IFAS Nat Coast Biol Stn, Cedar Key, FL USA.
   Nedelec, Sophie L., Univ Exeter, Coll Life \& Environm Sci, Biosci, Hatherly Labs, Exeter, Devon, England.
   Van Opzeeland, Ilse, Helmholtz Zentrum Polar \& Marine Res, Ocean Acoust Lab, Alfred Wegener Inst, Bremerhaven, Germany.
   Van Opzeeland, Ilse, Carl von Ossietzky Univ Oldenburg, Helmholtz Inst Funct Marine Biodivers HIFMB, Oldenburg, Germany.
   Radford, Craig, Univ Auckland, Inst Marine Sci, Leigh Marine Lab, Warkworth, New Zealand.
   Rice, Aaron N., Cornell Univ, Cornell Lab Ornithol, K Lisa Yang Ctr Conservat Bioacoust, Ithaca, NY USA.
   Sayigh, Laela, Hampshire Coll, Amherst, MA 01002 USA.
   Stanley, Jenni, Univ Waikato, Sch Sci, Coastal Marine Field Stn, Tauranga, New Zealand.
   Urban, Edward, Univ Delaware, Sci Comm Ocean Res, Newark, DE USA.
   Di Iorio, Lucia, Univ Perpignan Via Domitia, CNRS, Ctr Format \& Rech Sur Environm Mediterraneens, Perpignan, France.
   Di Iorio, Lucia, CHORUS Inst, Grenoble, France.},
DOI = {10.3389/fevo.2022.810156},
Article-Number = {810156},
ISSN = {2296-701X},
Keywords = {soundscape; bioacoustics database; artificial intelligence;
   biodiversity; passive acoustic monitoring; ecological informatics},
Keywords-Plus = {MULLOWAY ARGYROSOMUS-JAPONICUS; BOTTLE-NOSED DOLPHINS;
   OPHIDION-MARGINATUM OPHIDIIDAE; FISH SOUNDS; SPAWNING AGGREGATION;
   AUTOMATIC DETECTION; PASSIVE ACOUSTICS; WHALE SONG;
   BALAENOPTERA-PHYSALUS; MARINE MAMMALS},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {m.parsons@aims.gov.au},
Affiliations = {Australian Institute of Marine Science; Academia Sinica - Taiwan; Woods
   Hole Oceanographic Institution; Curtin University; University of
   Victoria; National Oceanic Atmospheric Admin (NOAA) - USA; Chinese
   Academy of Sciences; Institute of Deep-Sea Science \& Engineering, CAS;
   Commonwealth Scientific \& Industrial Research Organisation (CSIRO);
   State University System of Florida; University of Florida; State
   University System of Florida; University of Florida; University of
   Exeter; Helmholtz Association; Alfred Wegener Institute, Helmholtz
   Centre for Polar \& Marine Research; Carl von Ossietzky Universitat
   Oldenburg; University of Auckland; Cornell University; University of
   Waikato; University of Delaware; Centre National de la Recherche
   Scientifique (CNRS)},
ResearcherID-Numbers = {Barrela, Cristina/HJY-8958-2023
   Lin, Tzu-Hao/GLT-9168-2022
   Erbe, Christine/AAA-3801-2021
   Li, Songhai/A-2652-2012
   Rice, Aaron N/A-1292-2007
   Linke, Simon/G-5440-2010
   },
ORCID-Numbers = {Lin, Tzu-Hao/0000-0002-6973-3953
   Erbe, Christine/0000-0002-7884-9907
   Li, Songhai/0000-0003-4977-1722
   Looby, Audrey/0000-0003-1833-8643
   Linke, Simon/0000-0002-1797-3947
   Di Iorio, Lucia/0000-0002-3354-830X},
Funding-Acknowledgement = {U.S. National Science Foundation {[}OCE-1840868]},
Funding-Text = {Support for the initial author group to meet, discuss, and build
   consensus on the issues within this manuscript was provided by the
   Scientific Committee on Oceanic Research, Monmouth University Urban
   Coast Institute, and Rockefeller Program for the Human Environment. The
   U.S. National Science Foundation supported the publication of this
   article through Grant OCE-1840868 to the Scientific Committee on Oceanic
   Research.},
Number-of-Cited-References = {270},
Times-Cited = {17},
Usage-Count-Last-180-days = {8},
Usage-Count-Since-2013 = {48},
Journal-ISO = {Front. Ecol. Evol.},
Doc-Delivery-Number = {ZG9RI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000760587900001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000691830700009,
Author = {Prinja, Shankar and Dixit, Jyoti and Gupta, Nidhi and Mehra, Nikita and
   Singh, Ashish and Krishnamurthy, Manjunath Nookala and Gupta, Dharna and
   Rajsekar, Kavitha and Kalaiyarasi, Jayachandran Perumal and Roy, Partha
   Sarathi and Malik, Prabhat Singh and Mathew, Anisha and Pandey, Awadhesh
   and Malhotra, Pankaj and Gupta, Sudeep and Kumar, Lalit and Kataki, Amal
   and Singh, Gurpreet},
Title = {Development of National Cancer Database for Cost and Quality of Life
   (CaDCQoL) in India: a protocol},
Journal = {BMJ OPEN},
Year = {2021},
Volume = {11},
Number = {7},
Abstract = {Introduction The rising economic burden of cancer on healthcare system
   and patients in India has led to the increased demand for evidence in
   order to inform policy decisions such as drug price regulation, setting
   reimbursement package rates under publicly financed health insurance
   schemes and prioritising available resources to maximise value of
   investments in health. Economic evaluations are an integral component of
   this important evidence. Lack of existing evidence on healthcare costs
   and health-related quality of life (HRQOL) makes conducting economic
   evaluations a very challenging task. Therefore, it is imperative to
   develop a national database for health expenditure and HRQOL for cancer.
   Methods and analysis The present study proposes to develop a National
   Cancer Database for Cost and Quality of Life (CaDCQoL) in India. The
   healthcare costs will be estimated using a patient perspective. A
   cross-sectional study will be conducted to assess the direct
   out-of-pocket expenditure (OOPE), indirect cost and HRQOL among cancer
   patients who will be recruited at seven leading cancer centres from six
   states in India. Mean OOPE and HRQOL scores will be estimated by cancer
   site, stage of disease and type of treatment. Economic impact of cancer
   care on household financial risk protection will be assessed by
   estimating prevalence of catastrophic health expenditures and
   impoverishment. The national database would serve as a unique open
   access data repository to derive estimates of cancer-related OOPE and
   HRQOL. These estimates would be useful in conducting future
   cost-effectiveness analyses of management strategies for value-based
   cancer care. Ethics and dissemination Approval was granted by
   Institutional Ethics Committee vide letter no. PGI/IEC-03/2020-1565 of
   Post Graduate Institute of Medical Education and Research, Chandigarh,
   India. The study results will be published in peer-reviewed journals and
   presented to the policymakers at national level.},
Publisher = {BMJ PUBLISHING GROUP},
Address = {BRITISH MED ASSOC HOUSE, TAVISTOCK SQUARE, LONDON WC1H 9JR, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Prinja, S (Corresponding Author), Post Grad Inst Med Educ \& Res, Dept Community Med, Chandigarh, India.
   Prinja, S (Corresponding Author), Post Grad Inst Med Educ \& Res, Sch Publ Hlth, Chandigarh, India.
   Prinja, Shankar; Dixit, Jyoti; Gupta, Dharna, Post Grad Inst Med Educ \& Res, Dept Community Med, Chandigarh, India.
   Prinja, Shankar; Dixit, Jyoti; Gupta, Dharna, Post Grad Inst Med Educ \& Res, Sch Publ Hlth, Chandigarh, India.
   Gupta, Nidhi, Govt Med Coll \& Hosp, Dept Radiat Oncol, Chandigarh, India.
   Mehra, Nikita; Kalaiyarasi, Jayachandran Perumal, Canc Inst WIA, Dept Med Oncol, Chennai, Tamil Nadu, India.
   Singh, Ashish, Christian Med Coll Vellore, Dept Med Oncol, Vellore, Tamil Nadu, India.
   Krishnamurthy, Manjunath Nookala, Tata Mem Hosp, Dept Clin Pharmacol, Mumbai, Maharashtra, India.
   Rajsekar, Kavitha, India Minist Hlth \& Family Welf, Dept Hlth Res, Delhi, India.
   Roy, Partha Sarathi, Dr B Borooah Canc Soc Trust, Dept Med Oncol, Gauhati, Assam, India.
   Malik, Prabhat Singh; Mathew, Anisha; Kumar, Lalit, AIIMS, Dept Med Oncol, Delhi, India.
   Pandey, Awadhesh, Govt Med Coll \& Hosp, Radiotherapy \& Oncol, Chandigarh, India.
   Malhotra, Pankaj, Post Grad Inst Med Educ \& Res, Dept Internal Med, Chandigarh, India.
   Gupta, Sudeep, Tata Mem Hosp, Med Oncol, Mumbai, Maharashtra, India.
   Kataki, Amal, Dr B Borooah Canc Soc Trust, Dept Gynaecol Oncol, Gauhati, Assam, India.
   Singh, Gurpreet, Post Grad Inst Med Educ \& Res, Dept Gen Surg, Chandigarh, India.},
DOI = {10.1136/bmjopen-2020-048513},
Article-Number = {e048513},
ISSN = {2044-6055},
Keywords = {health economics; protocols \& guidelines; public health; radiation
   oncology; health policy},
Keywords-Plus = {ECONOMIC-EVALUATION; CHILDREN; EUROQOL; EQ-5D},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {shankarprinja@gmail.com},
Affiliations = {Post Graduate Institute of Medical Education \& Research (PGIMER),
   Chandigarh; Post Graduate Institute of Medical Education \& Research
   (PGIMER), Chandigarh; Christian Medical College \& Hospital (CMCH)
   Vellore; Tata Memorial Centre (TMC); Tata Memorial Hospital; All India
   Institute of Medical Sciences (AIIMS) New Delhi; Post Graduate Institute
   of Medical Education \& Research (PGIMER), Chandigarh; Tata Memorial
   Centre (TMC); Tata Memorial Hospital; Post Graduate Institute of Medical
   Education \& Research (PGIMER), Chandigarh},
ResearcherID-Numbers = {Kumar, Lalit/JFK-9602-2023
   Perumal Kalaiyarasi, Jayachandran/HLP-7438-2023
   },
ORCID-Numbers = {Gupta, Dharna/0000-0003-1954-6698
   Prinja, Shankar/0000-0001-7719-6986},
Funding-Acknowledgement = {Department of Health Research, Ministry of Health and Family Welfare,
   Government of India {[}F.T.11011/02/2017-HR/3100291]},
Funding-Text = {The study is funded by the Department of Health Research, Ministry of
   Health and Family Welfare, Government of India vide grant number
   F.No.T.11011/02/2017-HR/3100291.},
Number-of-Cited-References = {49},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {BMJ Open},
Doc-Delivery-Number = {UK2US},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000691830700009},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000814716800022,
Author = {Westbrook, John D. and Young, Jasmine Y. and Shao, Chenghua and Feng,
   Zukang and Guranovic, Vladimir and Lawson, Catherine L. and Vallat,
   Brinda and Adams, Paul D. and Berrisford, John M. and Bricogne, Gerard
   and Diederichs, Kay and Joosten, Robbie P. and Keller, Peter and
   Moriarty, Nigel W. and Sobolev, V, Oleg and Velankar, Sameer and
   Vonrhein, Clemens and Waterman, David G. and Kurisu, Genji and Berman,
   Helen M. and Burley, Stephen K. and Peisach, Ezra},
Title = {PDBx/mmCIF Ecosystem: Foundational Semantic Tools for Structural Biology},
Journal = {JOURNAL OF MOLECULAR BIOLOGY},
Year = {2022},
Volume = {434},
Number = {11},
Month = {JUN 15},
Abstract = {PDBx/mmCIF, Protein Data Bank Exchange (PDBx) macromolecular
   Crystallographic Information Framework (mmCIF), has become the data
   standard for structural biology. With its early roots in the domain of
   small-molecule crystallography, PDBx/mmCIF provides an extensible data
   representation that is used for deposition, archiving, remediation, and
   public dissemination of experimentally determined threedimensional (3D)
   structures of biological macromolecules by the Worldwide Protein Data
   Bank (wwPDB, wwpdb.org). Extensions of PDBx/mmCIF are similarly used for
   computed structure models by ModelArchive (modelarchive.org),
   integrative/hybrid structures by PDB-Dev (pdb-dev.wwpdb.org), small
   angle scattering data by Small Angle Scattering Biological Data Bank
   SASBDB (sasbdb.org), and for models computed generated with the
   AlphaFold 2.0 deep learning software suite (alphafold.ebi.ac.uk).
   Community-driven development of PDBx/mmCIF spans three decades,
   involving contributions from researchers, software and methods
   developers in structural sciences, data repository providers, scientific
   publishers, and professional societies. Having a semantically rich and
   extensible data framework for representing a wide range of structural
   biology experimental and computational results, combined with expertly
   curated 3D biostructure data sets in public repositories, accelerates
   the pace of scientific discovery. Herein, we describe the architecture
   of the PDBx/mmCIF data standard, tools used to maintain representations
   of the data standard, governance, and processes by which data content
   standards are extended, plus community tools/software libraries
   available for processing and checking the integrity of PDBx/mmCIF data.
   Use cases exemplify how the members of the Worldwide Protein Data Bank
   have used PDBx/mmCIF as the foundation for its pipeline for delivering
   Findable, Accessible, Interoperable, and Reusable (FAIR) data to many
   millions of users worldwide.(c) 2022 The Authors. Published by Elsevier
   Ltd. This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0},
Publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD},
Address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Burley, SK; Peisach, E (Corresponding Author), Rutgers State Univ, Inst Quantitat Biomed, Piscataway, NJ 08854 USA.
   Westbrook, John D.; Young, Jasmine Y.; Shao, Chenghua; Feng, Zukang; Guranovic, Vladimir; Lawson, Catherine L.; Vallat, Brinda; Berman, Helen M.; Burley, Stephen K.; Peisach, Ezra, Rutgers State Univ, Res Collaboratory Struct Bioinformat Prot Data Ba, Piscataway, NJ 08854 USA.
   Westbrook, John D.; Young, Jasmine Y.; Shao, Chenghua; Feng, Zukang; Guranovic, Vladimir; Lawson, Catherine L.; Vallat, Brinda; Burley, Stephen K.; Peisach, Ezra, Rutgers State Univ, Inst Quantitat Biomed, Piscataway, NJ 08854 USA.
   Westbrook, John D.; Burley, Stephen K., Rutgers State Univ, Canc Inst New Jersey, New Brunswick, NJ 08901 USA.
   Adams, Paul D.; Moriarty, Nigel W.; Sobolev, Oleg, V, Lawrence Berkeley Natl Laboratoty, Mol Biophys \& Integrated Bioimaging, Berkeley, CA 94720 USA.
   Adams, Paul D., Univ Calif Berkeley, Dept Bioengn, Berkeley, CA 94720 USA.
   Berrisford, John M.; Velankar, Sameer, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Prot Data Bank Europe, Wellcome Genome Campus, Cambridge CB10 1SD, England.
   Bricogne, Gerard; Keller, Peter; Vonrhein, Clemens, Global Phasing Ltd, Sheraton House,Castle Pk, Cambridge CB3 0AK, England.
   Diederichs, Kay, Univ Konstanz, D-78457 Constance, Germany.
   Joosten, Robbie P., Netherlands Canc Inst, Dept Biochem, Amsterdam, Netherlands.
   Joosten, Robbie P., Oncode Inst, NL-3521 AL Utrecht, Netherlands.
   Waterman, David G., UKRI STFC Rutherford Appleton Lab, Didcot OX11 0FA, Oxon, England.
   Waterman, David G., Rutherford Appleton Lab, CCP4,Res Complex Harwell, Didcot OX11 0FA, Oxon, England.
   Kurisu, Genji, Osaka Univ, Inst Prot Res, Prot Data Bank Japan, Suita, Osaka 5650871, Japan.
   Berman, Helen M.; Burley, Stephen K., Rutgers State Univ, Dept Chem \& Chem Biol, Piscataway, NJ 08854 USA.
   Berman, Helen M., Univ Southern Calif, Michelson Ctr Convergent Biosci, Bridge Inst, Los Angeles, CA 90007 USA.
   Burley, Stephen K., Univ Calif San Diego, San Diego Supercomp Ctr, Res Collaboratory Struct Bioinformat Prot Data Ba, La Jolla, CA 92093 USA.},
DOI = {10.1016/j.jmb.2022.167599},
EarlyAccessDate = {JUN 2022},
Article-Number = {167599},
ISSN = {0022-2836},
EISSN = {1089-8638},
Keywords = {data standard; protein data bank (PDB); biological data; data
   management; macromolecular structure},
Keywords-Plus = {MACROMOLECULAR STRUCTURE DATA; VISUALIZATION SYSTEM; PROTEIN;
   VALIDATION; CIF; PDB; REPRESENTATION; INTEGRATION; MOLECULES; ARCHIVE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {stephen.burley@rcsb.org
   ezra.peisach@rcsb.org},
Affiliations = {Rutgers System; Rutgers New Brunswick; Rutgers System; Rutgers New
   Brunswick; Rutgers System; Rutgers New Brunswick; Rutgers Biomedical \&
   Health Sciences; Rutgers Cancer Institute of New Jersey; United States
   Department of Energy (DOE); Lawrence Berkeley National Laboratory;
   University of California System; University of California Berkeley;
   European Molecular Biology Laboratory (EMBL); Global Phasing Limited;
   University of Konstanz; Netherlands Cancer Institute; UK Research \&
   Innovation (UKRI); Science \& Technology Facilities Council (STFC); STFC
   Rutherford Appleton Laboratory; UK Research \& Innovation (UKRI);
   Science \& Technology Facilities Council (STFC); STFC Rutherford
   Appleton Laboratory; Osaka University; Rutgers System; Rutgers New
   Brunswick; University of Southern California; University of California
   System; University of California San Diego},
ResearcherID-Numbers = {Adams, Paul David/A-1977-2013
   KURISU, GENJI/AAD-7109-2022
   Sobolev, Oleg V./O-2215-2013
   Moriarty, Nigel/AAH-2190-2019
   },
ORCID-Numbers = {Adams, Paul David/0000-0001-9333-8219
   KURISU, GENJI/0000-0002-5354-0807
   Sobolev, Oleg V./0000-0002-0623-3214
   Guranovic, Vladimir/0000-0001-7648-4628
   Velankar, Sameer/0000-0002-8439-5964
   Moriarty, Nigel/0000-0001-8857-9464
   Shao, Chenghua/0000-0001-6817-7476},
Funding-Acknowledgement = {National Science Foundation {[}DBI-1832184]; US Department of Energy
   {[}DE-SC0019749]; National Cancer Institute, National Institute of
   Allergy and Infectious Diseases; National Institute of General Medical
   Sciences of the National Institutes of Health {[}BB/M013146/1,
   BB/M011674/1]; European Molecular Biology Laboratory-European
   Bioinformatics Institute {[}BB/M013146/1, BB/M011674/1, BB/K016970/1,
   BB/K020013/1, BB/M020347/1, BB/M020428/1, BB/P024351/1, R01GM133198,
   DBI-2019297, 104948]; European Molecular Biology Laboratory-European
   Bioinformatics Institute; Wellcome Trust; Biotechnology and Biological
   Sciences Research Council; European Union {[}BB/M020347/1]; ELIXIR
   {[}BB/K016970/1, BB/K020013/1, BB/M020428/1, BB/P024351/1, R01GM133198,
   DBI-2019297, 104948, BB/N019172/1, BB/G022577/1, BB/J007471/1]; Open
   Targets {[}BB/M013146/1]; NBDC-JST; BINDS-AMED;  {[}284209]},
Funding-Text = {RCSB PDB is funded by the National Science Foundation {[}DBI-1832184;
   P.I.: S.K.B.] , the US Department of Energy {[}DE-SC0019749; P.I.: S.K.
   B.] , and the National Cancer Institute, National Institute of Allergy
   and Infectious Diseases, and National Institute of General Medical
   Sciences of the National Institutes of Health {[}R01GM133198; P.I.:
   S.K.B.] . Development of the PDBx/mmCIF data dictionary is funded in
   part by {[}DBI-2019297; P.I.: S.K.B.] . PDBe is funded by European
   Molecular Biology Laboratory-European Bioinformatics Institute; Wellcome
   Trust {[}104948] ; Biotechnology and Biological Sciences Research
   Council {[}BB/N019172/1, BB/G022577/1, BB/J007471/1, BB/K016970/1,
   BB/K020013/1, BB/M013146/1, BB/M011674/1, BB/M020347/1, BB/M020428/1,
   BB/P024351/1] ; European Union {[}284209] ; ELIXIR; and Open Targets.
   PDBj is funded by the NBDC-JST {[}P.I.: G.K.] , partially by BINDS-AMED
   {[}P.I.: G.K.] . The authors would like to acknowledge the early work by
   Syd Hall, Paula Fitzgerald, and Brian McMahon, Keith Watenpaugh, Phil
   Bourne and many others who were instrumental in the development of the
   original mmCIF data standard.},
Number-of-Cited-References = {68},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Mol. Biol.},
Doc-Delivery-Number = {2I1AU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000814716800022},
OA = {Green Accepted, hybrid, Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000661074700032,
Author = {Kudla, Mateusz and Gutowska, Kaja and Synak, Jaroslaw and Weber, Mirko
   and Bohnsack, Katrin Sophie and Lukasiak, Piotr and Villmann, Thomas and
   Blazewicz, Jacek and Szachniuk, Marta},
Title = {Virxicon: a lexicon of viral sequences},
Journal = {BIOINFORMATICS},
Year = {2020},
Volume = {36},
Number = {22-23},
Pages = {5507-5513},
Month = {DEC 1},
Abstract = {Motivation: Viruses are the most abundant biological entities and
   constitute a large reservoir of genetic diversity. In recent years,
   knowledge about them has increased significantly as a result of dynamic
   development in life sciences and rapid technological progress. This
   knowledge is scattered across various data repositories, making a
   comprehensive analysis of viral data difficult.
   Results: In response to the need for gathering a comprehensive knowledge
   of viruses and viral sequences, we developed Virxicon, a lexicon of all
   experimentally acquired sequences for RNA and DNA viruses. The ability
   to quickly obtain data for entire viral groups, searching sequences by
   levels of taxonomic hierarchy-according to the Baltimore classification
   and ICTV taxonomy-and tracking the distribution of viral data and its
   growth over time are unique features of our database compared to the
   other tools.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Szachniuk, M (Corresponding Author), Poznan Univ Tech, Inst Comp Sci, PL-60965 Poznan, Poland.
   Szachniuk, M (Corresponding Author), Poznan Univ Tech, European Ctr Bioinformat \& Genom, PL-60965 Poznan, Poland.
   Szachniuk, M (Corresponding Author), Polish Acad Sci, Inst Bioorgan Chem, Dept Struct Bioinformat, PL-61704 Poznan, Poland.
   Kudla, Mateusz; Gutowska, Kaja; Synak, Jaroslaw; Lukasiak, Piotr; Blazewicz, Jacek; Szachniuk, Marta, Poznan Univ Tech, Inst Comp Sci, PL-60965 Poznan, Poland.
   Kudla, Mateusz; Gutowska, Kaja; Synak, Jaroslaw; Lukasiak, Piotr; Blazewicz, Jacek; Szachniuk, Marta, Poznan Univ Tech, European Ctr Bioinformat \& Genom, PL-60965 Poznan, Poland.
   Kudla, Mateusz; Weber, Mirko; Bohnsack, Katrin Sophie; Villmann, Thomas, Univ Appl Sci Mittweida, Saxon Inst Computat Intelligence \& Machine Learni, D-09648 Mittweida, Germany.
   Gutowska, Kaja; Lukasiak, Piotr; Blazewicz, Jacek; Szachniuk, Marta, Polish Acad Sci, Inst Bioorgan Chem, Dept Struct Bioinformat, PL-61704 Poznan, Poland.},
DOI = {10.1093/bioinformatics/btaa1066},
ISSN = {1367-4803},
EISSN = {1367-4811},
Keywords-Plus = {RESPIRATORY SYNDROME CORONAVIRUS; VIRUS; TRANSMISSION; DATABASE;
   GENOMES; RESOURCE; WEB},
Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
   Microbiology; Computer Science; Mathematical \& Computational Biology;
   Mathematics},
Web-of-Science-Categories  = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
   Computer Science, Interdisciplinary Applications; Mathematical \&
   Computational Biology; Statistics \& Probability},
Author-Email = {mszachniuk@cs.put.poznan.pl},
Affiliations = {Poznan University of Technology; Poznan University of Technology; Polish
   Academy of Sciences; Institute of Bioorganic Chemistry of the Polish
   Academy of Sciences},
ResearcherID-Numbers = {Szachniuk, Marta/N-1991-2014
   Blazewicz, Jacek/L-5597-2014
   Synak, Jaroslaw/AAI-3858-2021
   },
ORCID-Numbers = {Szachniuk, Marta/0000-0002-8724-7908
   Blazewicz, Jacek/0000-0001-8326-1094
   Gutowska, Kaja/0000-0002-5733-8809
   Lukasiak, Piotr/0000-0003-4012-9135
   Bohnsack, Katrin Sophie/0000-0002-2361-107X},
Funding-Acknowledgement = {National Science Centre, Poland {[}2016/23/B/ST6/03931,
   2019/35/B/ST6/03074]; Poznan University of Technology; European Social
   Fund (ESF); Institute of Bioorganic Chemistry, Polish Academy of
   Sciences},
Funding-Text = {This project was supported by the National Science Centre, Poland
   {[}2016/23/B/ST6/03931, 2019/35/B/ST6/03074], the statutory funds of
   Poznan University of Technology and the grant of the European Social
   Fund (ESF). Funding for open access charge: Institute of Bioorganic
   Chemistry, Polish Academy of Sciences.},
Number-of-Cited-References = {41},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Bioinformatics},
Doc-Delivery-Number = {SR5IJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000661074700032},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000425027700008,
Author = {Nielsen, Jens M. and Clare, Elizabeth L. and Hayden, Brian and Brett,
   Michael T. and Kratina, Pavel},
Title = {Diet tracing in ecology: Method comparison and selection},
Journal = {METHODS IN ECOLOGY AND EVOLUTION},
Year = {2018},
Volume = {9},
Number = {2},
Pages = {278-291},
Month = {FEB},
Abstract = {1. Determining diet is a key prerequisite for understanding species
   interactions, food web structure and ecological dynamics. In recent
   years, there has been considerable development in both the methodology
   and application of novel and more traditional dietary tracing methods,
   yet there is no comprehensive synthesis that systematically and
   quantitatively compares the different approaches.
   2. Here we conceptualise diet tracing in ecology, provide
   recommendations for method selection, and illustrate the advantages of
   method integration. We summarise empirical evidence on how different
   methods quantify diet mixtures, by contrasting estimates of dietary
   proportions from multiple methods applied to the same consumer-resource
   datasets, or from experimental studies with known diet compositions.
   3. Our data synthesis revealed an urgent need for more experiential
   comparisons among the dietary methods. The comparison of diet
   quantifications from field observations showed that different techniques
   aligned well in cases with less than six diet items, but diverged
   considerably when applied to more complex diet mixtures.
   4. Efforts are ongoing to further advance dietary estimation, including
   how reliably compound specific stable isotope analyses and fatty acid
   profiles can quantify more prey items than bulk stable isotope analyses.
   Similarly, DNA analyses, which can depict trophic interactions at a
   higher resolution than any other method, are generating new ways to
   better quantify diets and differentiate among life-stages of prey. Such
   efforts, combined with more empirical testing of each dietary method and
   establishment of open data repositories for dietary data, promise to
   greatly advance community and ecosystem ecology.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Review},
Language = {English},
Affiliation = {Nielsen, JM; Kratina, P (Corresponding Author), Queen Mary Univ London, Sch Biol \& Chem Sci, London, England.
   Nielsen, JM (Corresponding Author), Univ Washington, Dept Civil \& Environm Engn, Seattle, WA 98195 USA.
   Nielsen, Jens M.; Clare, Elizabeth L.; Kratina, Pavel, Queen Mary Univ London, Sch Biol \& Chem Sci, London, England.
   Hayden, Brian, Univ New Brunswick, Canadian Rivers Inst, Biol Dept, Fredericton, NB, Canada.
   Nielsen, Jens M.; Brett, Michael T., Univ Washington, Dept Civil \& Environm Engn, Seattle, WA 98195 USA.},
DOI = {10.1111/2041-210X.12869},
ISSN = {2041-210X},
EISSN = {2041-2096},
Keywords = {biomarkers; compound-specific stable isotopes; diet analyses; fatty
   acids; food webs; molecular diet analyses; stable isotopes; stomach
   contents; trophic interactions},
Keywords-Plus = {FOOD-WEB STRUCTURE; NITROGEN ISOTOPIC COMPOSITION; DNA-BASED DIET;
   STABLE-ISOTOPE; FATTY-ACIDS; AMINO-ACIDS; MOLECULAR-IDENTIFICATION;
   TROPHIC INTERACTIONS; CARBON; PHYTOPLANKTON},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {jensmunielsen@gmail.com
   p.kratina@qmul.ac.uk},
Affiliations = {University of London; Queen Mary University London; University of New
   Brunswick; University of Washington; University of Washington Seattle},
ResearcherID-Numbers = {Kratina, Pavel/O-5192-2019
   },
ORCID-Numbers = {Kratina, Pavel/0000-0002-9144-7937
   Brett, Michael/0000-0002-8796-9863},
Number-of-Cited-References = {121},
Times-Cited = {287},
Usage-Count-Last-180-days = {23},
Usage-Count-Since-2013 = {303},
Journal-ISO = {Methods Ecol. Evol.},
Doc-Delivery-Number = {FW1AN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000425027700008},
OA = {Bronze, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000429870700020,
Author = {Carter, Daniel J. and Glaziou, Philippe and Lonnroth, Knut and Siroka,
   Andrew and Floyd, Katherine and Weil, Diana and Raviglione, Mario and
   Houben, Rein M. G. J. and Boccia, Delia},
Title = {The impact of social protection and poverty elimination on global
   tuberculosis incidence: a statistical modelling analysis of Sustainable
   Development Goal 1},
Journal = {LANCET GLOBAL HEALTH},
Year = {2018},
Volume = {6},
Number = {5},
Pages = {E514-E522},
Month = {MAY},
Abstract = {Background The End TB Strategy and the Sustainable Development Goals
   (SDGs) are intimately linked by their common targets and approaches. SDG
   1 aims to end extreme poverty and expand social protection coverage by
   2030. Achievement of SDG 1 is likely to affect the tuberculosis epidemic
   through a range of pathways. We estimate the reduction in global
   tuberculosis incidence that could be obtained by reaching SDG 1.
   Methods We developed a conceptual framework linking key indicators of
   SDG 1 progress to tuberculosis incidence via well described risk factor
   pathways and populated it with data from the SDG data repository and the
   WHO tuberculosis database for 192 countries. Correlations and mediation
   analyses informed the strength of the association between the SDG 1
   subtargets and tuberculosis incidence, resulting in a simplified
   framework for modelling. The simplified framework linked key indicators
   for SDG 1 directly to tuberculosis incidence. We applied an exponential
   decay model based on linear associations between SDG 1 indicators and
   tuberculosis incidence to estimate tuberculosis incidence in 2035.
   Findings Ending extreme poverty resulted in a reduction in global
   incidence of tuberculosis of 33.4\% (95\% credible interval 15.5-44.5)
   by 2035 and expanding social protection coverage resulted in a reduction
   in incidence of 76.1\% (45.2-89.9) by 2035; both pathways together
   resulted in a reduction in incidence of 84.3\% (54.7-94.9).
   Interpretation Full achievement of SDG 1 could have a substantial effect
   on the global burden of tuberculosis. Cross-sectoral approaches that
   promote poverty reduction and social protection expansion will be
   crucial complements to health interventions, accelerating progress
   towards the End TB targets. Copyright (c) The Author(s). Published by
   Elsevier Ltd. This is an Open Access article under the CC BY-NC-ND 4.0
   license.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Carter, DJ (Corresponding Author), London Sch Hyg \& Trop Med, Dept Infect Dis Epidemiol, London WC1E 7HT, England.
   Carter, Daniel J.; Boccia, Delia, London Sch Hyg \& Trop Med, Dept Infect Dis Epidemiol, London WC1E 7HT, England.
   Houben, Rein M. G. J., London Sch Hyg \& Trop Med, TB Modelling Grp, TB Ctr, London, England.
   Glaziou, Philippe; Siroka, Andrew; Floyd, Katherine; Weil, Diana; Raviglione, Mario, WHO, Global TB Programme, Geneva, Switzerland.
   Raviglione, Mario, Univ Milan, Dept Global Hlth, Milan, Italy.
   Lonnroth, Knut, Karolinska Inst, Dept Publ Hlth Sci, Stockholm, Sweden.},
DOI = {10.1016/S2214-109X(18)30195-5},
ISSN = {2214-109X},
Keywords-Plus = {END TB STRATEGY},
Research-Areas = {Public, Environmental \& Occupational Health},
Web-of-Science-Categories  = {Public, Environmental \& Occupational Health},
Author-Email = {daniel.carter1@lshtm.ac.uk},
Affiliations = {University of London; London School of Hygiene \& Tropical Medicine;
   University of London; London School of Hygiene \& Tropical Medicine;
   World Health Organization; University of Milan; Karolinska Institutet},
ResearcherID-Numbers = {Lonnroth, Knut/H-5470-2017
   },
ORCID-Numbers = {Lonnroth, Knut/0000-0001-6944-0256
   Glaziou, Philippe/0000-0002-0649-1272},
Funding-Acknowledgement = {World Health Organization},
Funding-Text = {World Health Organization.},
Number-of-Cited-References = {18},
Times-Cited = {77},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {28},
Journal-ISO = {Lancet Glob. Health},
Doc-Delivery-Number = {GC5ZU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000429870700020},
OA = {gold, Green Accepted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000299630600014,
Author = {Blankenberg, Daniel and Coraor, Nathan and Von Kuster, Gregory and
   Taylor, James and Nekrutenko, Anton and Galaxy Team},
Title = {Integrating diverse databases into an unified analysis framework: a
   Galaxy approach},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2011},
Abstract = {Recent technological advances have lead to the ability to generate large
   amounts of data for model and non-model organisms. Whereas, in the past,
   there have been a relatively small number of central repositories that
   serve genomic data, an increasing number of distinct specialized data
   repositories and resources have been established. Here, we describe a
   generic approach that provides for the integration of a diverse spectrum
   of data resources into a unified analysis framework, Galaxy
   (http://usegalaxy.org). This approach allows the simplified coupling of
   external data resources with the data analysis tools available to Galaxy
   users, while leveraging the native data mining facilities of the
   external data resources.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Nekrutenko, A (Corresponding Author), Penn State Univ, Galaxy Project, University Pk, PA 16802 USA.
   Blankenberg, Daniel; Coraor, Nathan; Von Kuster, Gregory; Taylor, James; Nekrutenko, Anton, Penn State Univ, Galaxy Project, University Pk, PA 16802 USA.
   Blankenberg, Daniel; Coraor, Nathan; Von Kuster, Gregory; Nekrutenko, Anton, Penn State Univ, Huck Inst Life Sci, Dept Biochem \& Mol Biol, University Pk, PA 16802 USA.
   Taylor, James, Emory Univ, Dept Biol, Atlanta, GA 30322 USA.
   Taylor, James, Emory Univ, Dept Math \& Comp Sci, Atlanta, GA 30322 USA.},
DOI = {10.1093/database/bar011},
Article-Number = {bar011},
ISSN = {1758-0463},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {dan@bx.psu.edu
   james.taylor@emory.edu
   anton@bx.psu.edu},
Affiliations = {Pennsylvania Commonwealth System of Higher Education (PCSHE);
   Pennsylvania State University; Pennsylvania State University -
   University Park; Pennsylvania Commonwealth System of Higher Education
   (PCSHE); Pennsylvania State University; Pennsylvania State University -
   University Park; Emory University; Emory University},
ResearcherID-Numbers = {Taylor, James/F-1026-2011
   },
ORCID-Numbers = {Taylor, James/0000-0001-5079-840X
   Nekrutenko, Anton/0000-0002-5987-8032
   Blankenberg, Daniel/0000-0002-6833-9049},
Funding-Acknowledgement = {Beckman Foundation; National Science Foundation {[}DBI 0543285];
   National Institutes of Health {[}HG004909, HG005133, HG005542]; Penn
   State University; Huck Institutes for the Life Sciences; Emory
   University; Pennsylvania Department of Health; Div Of Biological
   Infrastructure; Direct For Biological Sciences {[}0850103] Funding
   Source: National Science Foundation},
Funding-Text = {The Beckman Foundation Young Investigator Award (to A.N.); National
   Science Foundation (DBI 0543285) and National Institutes of Health
   (HG004909 to A.N. and J.T.); National Institutes of Health (HG005133 and
   HG005542 to J.T. and A.N.); the Penn State University and the Huck
   Institutes for the Life Sciences (to A.N.); the Emory University (to
   J.T.). Additional funding is provided, in part, under a grant with the
   Pennsylvania Department of Health using Tobacco Settlement Funds. The
   Department specifically disclaims responsibility for any analyses,
   interpretations or conclusions. Funding for open access charge: Penn
   State University.},
Number-of-Cited-References = {14},
Times-Cited = {30},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Database},
Doc-Delivery-Number = {883JQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000299630600014},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000312893300151,
Author = {Vizcaino, Juan Antonio and Cote, Richard G. and Csordas, Attila and
   Dianes, Jose A. and Fabregat, Antonio and Foster, Joseph M. and Griss,
   Johannes and Alpi, Emanuele and Birim, Melih and Contell, Javier and
   O'Kelly, Gavin and Schoenegger, Andreas and Ovelleiro, David and
   Perez-Riverol, Yasset and Reisinger, Florian and Rios, Daniel and Wang,
   Rui and Hermjakob, Henning},
Title = {The Proteomics Identifications (PRIDE) database and associated tools:
   status in 2013},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2013},
Volume = {41},
Number = {D1},
Pages = {D1063-D1069},
Month = {JAN},
Abstract = {The PRoteomics IDEntifications (PRIDE, http://www.ebi.ac.uk/pride)
   database at the European Bioinformatics Institute is one of the most
   prominent data repositories of mass spectrometry (MS)-based proteomics
   data. Here, we summarize recent developments in the PRIDE database and
   related tools. First, we provide up-to-date statistics in data content,
   splitting the figures by groups of organisms and species, including
   peptide and protein identifications, and post-translational
   modifications. We then describe the tools that are part of the PRIDE
   submission pipeline, especially the recently developed PRIDE Converter 2
   (new submission tool) and PRIDE Inspector (visualization and analysis
   tool). We also give an update about the integration of PRIDE with other
   MS proteomics resources in the context of the ProteomeXchange
   consortium. Finally, we briefly review the quality control efforts that
   are ongoing at present and outline our future plans.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Vizcaíno, JA (Corresponding Author), European Bioinformat Inst, EMBL Outstn, Wellcome Trust Genome Campus, Cambridge, England.
   Vizcaino, Juan Antonio; Cote, Richard G.; Csordas, Attila; Dianes, Jose A.; Fabregat, Antonio; Foster, Joseph M.; Griss, Johannes; Alpi, Emanuele; Birim, Melih; Contell, Javier; O'Kelly, Gavin; Schoenegger, Andreas; Ovelleiro, David; Perez-Riverol, Yasset; Reisinger, Florian; Rios, Daniel; Wang, Rui; Hermjakob, Henning, European Bioinformat Inst, EMBL Outstn, Cambridge, England.
   Perez-Riverol, Yasset, Ctr Genet Engn \& Biotechnol, Dept Prote, Havana, Cuba.
   Schoenegger, Andreas, Austrian Acad Sci, CeMM Res Ctr Mol Med, A-1090 Vienna, Austria.},
DOI = {10.1093/nar/gks1262},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PUBLIC REPOSITORY; PROTEIN; STANDARD; PEPTIDE; CONVERTER; VISUALIZE;
   FRAMEWORK; PLATFORM; SYSTEM; API},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {pst@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL); Centro de Ingenieria
   Genetica y Biotecnologia; Austrian Academy of Sciences; CeMM Research
   Center for Molecular Medicine of the Austrian Academy of Sciences},
ResearcherID-Numbers = {Perez-Riverol, Yasset/H-2873-2019
   Hermjakob, Henning/AFM-3497-2022
   Vizcaino, Juan Antonio/C-3691-2009
   },
ORCID-Numbers = {Perez-Riverol, Yasset/0000-0001-6579-6941
   Hermjakob, Henning/0000-0001-8479-0262
   Vizcaino, Juan Antonio/0000-0002-3905-4335
   Alpi, Emanuele/0000-0003-4822-9472
   Ovelleiro, David/0000-0002-9415-2229
   Dianes, Jose A/0000-0002-5904-9269
   Griss, Johannes/0000-0003-2206-9511
   Fabregat Mundo, Antonio/0000-0002-3288-8599},
Funding-Acknowledgement = {Wellcome Trust {[}WT085949MA]; EU {[}226073, 260558, 262067, 202272];
   BBSRC {[}BB/I024204/1]; EMBL; BBSRC {[}BB/I024204/1] Funding Source:
   UKRI; Biotechnology and Biological Sciences Research Council
   {[}BB/I024204/1] Funding Source: researchfish},
Funding-Text = {The PRIDE team is funded by the Wellcome Trust {[}WT085949MA]; EU FP7
   grants `Sling' {[}226073]; `ProteomeXchange' {[}260558]; `PRIME-XS'
   {[}262067]; `LipidomicNet' {[}202272]; BBSRC grant `PRIDE Converter'
   {[}reference BB/I024204/1] and EMBL core funding. Funding for open
   access charge: Wellcome Trust {[}WT085949MA].},
Number-of-Cited-References = {53},
Times-Cited = {1607},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {185},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {062BE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000312893300151},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000392838300008,
Author = {Ghose, Rina and Appel, Stephen},
Title = {Facilitating PPGIS Through University Libraries},
Journal = {CARTOGRAPHIC JOURNAL},
Year = {2016},
Volume = {53},
Number = {4, SI},
Pages = {341-347},
Month = {NOV},
Abstract = {Equitable access to local geospatial data continues to pose challenges
   to the knowledge production efforts of marginalized citizen groups.
   While local government agencies have provided greater access to public
   data sets through their internet Geographic Information System (GIS)
   sites, data cannot always be downloaded and used directly by citizens.
   Past research demonstrates that data sharing at the local level can be a
   challenging task, mired by legal, institutional, and personal issues.
   Despite the hype about open data in government, its acceptance and
   implementation is slow at the local scale. The need for a centralized
   data repository system at the local scale is thus crucial. This research
   explores the recent groundbreaking effort to establish a state-wide
   geospatial portal among the 26 University of Wisconsin (UW) library
   systems. Through a survey and follow up interviews conducted among
   public land information professionals in Wisconsin, we find that GIS
   professionals in local and county governments are open to data sharing
   through a common geospatial portal. Simultaneously, the efforts to
   introduce open source GIS software and technical skills through
   workshops conducted by the library staff demonstrate new ways to
   facilitate Public Participation GIS (PPGIS). Our research thus
   demonstrates that university libraries can emerge as an effective model
   for advancing PPGIS through geoportals, web services, and data and
   applications in the cloud.},
Publisher = {TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OR14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Ghose, R (Corresponding Author), Univ Wisconsin, Geog, Milwaukee, WI 53201 USA.
   Ghose, Rina, Univ Wisconsin, Geog, Milwaukee, WI 53201 USA.
   Appel, Stephen, Univ Wisconsin, Milwaukee, WI 53201 USA.},
DOI = {10.1080/00087041.2016.1227567},
ISSN = {0008-7041},
EISSN = {1743-2774},
Keywords = {public participation GIS; data access; open GIS},
Keywords-Plus = {SPATIAL DATA INFRASTRUCTURES; GIS; POLITICS},
Research-Areas = {Geography},
Web-of-Science-Categories  = {Geography},
Author-Email = {rghose@gmail.com},
Affiliations = {University of Wisconsin System; University of Wisconsin Milwaukee;
   University of Wisconsin System; University of Wisconsin Milwaukee},
ResearcherID-Numbers = {Appel, Stephen/GLT-1095-2022},
ORCID-Numbers = {Appel, Stephen/0000-0002-4976-8489},
Number-of-Cited-References = {28},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Cartogr. J.},
Doc-Delivery-Number = {EI9OR},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000392838300008},
DA = {2024-01-15},
}

@article{ WOS:001025008600001,
Author = {McKay, Francis and Williams, Bethany J. and Prestwich, Graham and
   Bansal, Daljeet and Treanor, Darren and Hallowell, Nina},
Title = {Artificial intelligence and medical research databases: ethical review
   by data access committees},
Journal = {BMC MEDICAL ETHICS},
Year = {2023},
Volume = {24},
Number = {1},
Month = {JUL 8},
Abstract = {BackgroundIt has been argued that ethics review committees-e.g.,
   Research Ethics Committees, Institutional Review Boards, etc.- have
   weaknesses in reviewing big data and artificial intelligence research.
   For instance, they may, due to the novelty of the area, lack the
   relevant expertise for judging collective risks and benefits of such
   research, or they may exempt it from review in instances involving
   de-identified data.Main bodyFocusing on the example of medical research
   databases we highlight here ethical issues around de-identified data
   sharing which motivate the need for review where oversight by ethics
   committees is weak. Though some argue for ethics committee reform to
   overcome these weaknesses, it is unclear whether or when that will
   happen. Hence, we argue that ethical review can be done by data access
   committees, since they have de facto purview of big data and artificial
   intelligence projects, relevant technical expertise and governance
   knowledge, and already take on some functions of ethical review. That
   said, like ethics committees, they may have functional weaknesses in
   their review capabilities. To strengthen that function, data access
   committees must think clearly about the kinds of ethical expertise, both
   professional and lay, that they draw upon to support their
   work.ConclusionData access committees can undertake ethical review of
   medical research databases provided they enhance that review function
   through professional and lay ethical expertise.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {McKay, F (Corresponding Author), Univ Newcastle, Populat Hlth Sci Inst, Newcastle Upon Tyne NE2 4AX, England.
   McKay, Francis, Univ Newcastle, Populat Hlth Sci Inst, Newcastle Upon Tyne NE2 4AX, England.
   Williams, Bethany J.; Bansal, Daljeet; Treanor, Darren, Leeds Teaching Hosp NHS Trust, Natl Pathol Imaging Cooperat, Leeds LS9 7TF, England.
   Prestwich, Graham, Unit 1, Yorkshire \& Humber Acad Hlth Sci Network, Unit 1, Calder Pk, Wakefield WF4 3BA, England.
   Treanor, Darren, Univ Leeds, Dept Pathol, Leeds, England.
   Treanor, Darren, Linkoping Univ, Dept Clin Pathol, Linkoping, Sweden.
   Treanor, Darren, Linkoping Univ, Ctr Med Image Sci \& Visualizat CMIV, Linkoping, Sweden.
   Hallowell, Nina, Univ Oxford, Ethox Ctr, Oxford OX3 7LF, England.
   Hallowell, Nina, Univ Oxford, Wellcome Ctr Eth \& Humanities, Nuffield Dept Populat Hlth, Oxford OX3 7LF, England.},
DOI = {10.1186/s12910-023-00927-8},
Article-Number = {49},
ISSN = {1472-6939},
Keywords = {Artificial intelligence; Medical research databases; Health data
   repositories; Data access committees; Research ethics committees;
   Ethical review; Ethical expertise; Public involvement},
Keywords-Plus = {GENOMIC DATA; PUBLIC INVOLVEMENT; HEALTH; OVERSIGHT; PATIENT; MEMBERS},
Research-Areas = {Social Sciences - Other Topics; Medical Ethics; Biomedical Social
   Sciences},
Web-of-Science-Categories  = {Ethics; Medical Ethics; Social Sciences, Biomedical},
Author-Email = {francis.mckay@newcastle.ac.uk},
Affiliations = {Newcastle University - UK; University of Leeds; University of Leeds;
   Linkoping University; Linkoping University; University of Oxford;
   University of Oxford},
ORCID-Numbers = {Mckay, Francis/0000-0002-3177-9446},
Funding-Acknowledgement = {National Pathology Imaging Cooperative, NPIC {[}104687]; Industrial
   Strategy Challenge Fund; Li Ka Shing Foundation; Wellcome Trust
   {[}203132]},
Funding-Text = {The authors of this study are members of the National Pathology Imaging
   Cooperative, NPIC (Project no. 104687) which is supported by a 50 m
   investment from the Data to Early Diagnosis and Precision Medicine
   strand of the government's Industrial Strategy Challenge Fund, managed
   and delivered by UK Research and Innovation (UKRI). NH's research is
   funded by the Li Ka Shing Foundation. Both NH and FM are also members of
   the Ethox Centre and the Wellcome Centre for Ethics and Humanities which
   is supported by funding from the Wellcome Trust (Grant no 203132). No
   specific funding was received for this study. For the purpose of Open
   Access, the author has applied a CC BY public copyright licence to any
   Author Accepted Manuscript (AAM) version arising from this submission.},
Number-of-Cited-References = {50},
Times-Cited = {1},
Usage-Count-Last-180-days = {12},
Usage-Count-Since-2013 = {12},
Journal-ISO = {BMC Med. Ethics},
Doc-Delivery-Number = {L7KJ5},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:001025008600001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000623721700002,
Author = {Khan, Nushrat and Thelwall, Mike and Kousha, Kayvan},
Title = {Measuring the impact of biodiversity datasets: data reuse, citations and
   altmetrics},
Journal = {SCIENTOMETRICS},
Year = {2021},
Volume = {126},
Number = {4},
Pages = {3621-3639},
Month = {APR},
Abstract = {Despite growing evidence of open biodiversity data reuse by scientists,
   information about how data is reused and cited is rarely openly
   accessible from research data repositories. This study explores data
   citation and reuse practices in biodiversity by using openly available
   metadata for 43,802 datasets indexed in the Global Biodiversity
   Information Facility (GBIF) and content analyses of articles citing GBIF
   data. Results from quantitative and content analyses suggest that even
   though the number of studies making use of openly available biodiversity
   data has been increasing steadily, best practice for data citation is
   not yet common. It is encouraging, however, that an increasing number of
   recent articles (16 out of 23 in 2019) in biodiversity cite datasets in
   a standard way. A content analysis of a random sample of unique citing
   articles (n = 100) found various types of background (n= 18) and
   foreground (n=81) reuse cases for GBIF data, ranging from combining with
   other data sources to create species distribution modelling to software
   testing. This demonstrates some unique research opportunities created by
   open data. Among the citing articles, 27\% mentioned the dataset in
   references and 13\% in data access statements in addition to the methods
   section. Citation practice was inconsistent especially when a large
   number of subsets (12 similar to 50) were used. Even though many GBIF
   dataset records had altmetric scores, most posts only mentioned the
   articles linked to those datasets. Among the altmetric mentions of
   datasets, blogs can be the most informative, even though rare, and most
   tweets and Facebook posts were for promotional purposes.},
Publisher = {SPRINGER},
Address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Khan, N (Corresponding Author), Univ Wolverhampton, Wulfruna St, Wolverhampton WV1 1LY, England.
   Khan, Nushrat; Thelwall, Mike; Kousha, Kayvan, Univ Wolverhampton, Wulfruna St, Wolverhampton WV1 1LY, England.},
DOI = {10.1007/s11192-021-03890-6},
EarlyAccessDate = {FEB 2021},
ISSN = {0138-9130},
EISSN = {1588-2861},
Keywords = {Open biodiversity data; Altmetrics; Data reuse; Citation practice;
   Citation analysis},
Research-Areas = {Computer Science; Information Science \& Library Science},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Information Science \&
   Library Science},
Author-Email = {n.j.khan@wlv.ac.uk
   m.thelwall@wlv.ac.uk
   k.kousha@wlv.ac.uk},
Affiliations = {University of Wolverhampton},
ResearcherID-Numbers = {Thelwall, Mike/C-1449-2013
   Thelwall, Mike/JDV-4700-2023
   Kousha, Kayvan/B-1937-2010
   Khan, Nushrat/JEZ-3760-2023
   },
ORCID-Numbers = {Thelwall, Mike/0000-0001-6065-205X
   Thelwall, Mike/0000-0001-6065-205X
   Khan, Nushrat/0000-0002-4521-0920
   Kousha, Kayvan/0000-0003-4827-971X},
Funding-Acknowledgement = {University of Wolverhampton},
Funding-Text = {This study was funded by the University of Wolverhampton.},
Number-of-Cited-References = {32},
Times-Cited = {8},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {61},
Journal-ISO = {Scientometrics},
Doc-Delivery-Number = {RK9JQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000623721700002},
OA = {Green Submitted, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000394777800020,
Author = {Bishop, Libby and Kuula-Lummi, Arja},
Title = {Revisiting Qualitative Data Reuse: A Decade On},
Journal = {SAGE OPEN},
Year = {2017},
Volume = {7},
Number = {1},
Month = {JAN},
Abstract = {Secondary analysis of qualitative data entails reusing data created from
   previous research projects for new purposes. Reuse provides an
   opportunity to study the raw materials of past research projects to gain
   methodological and substantive insights. In the past decade, use of the
   approach has grown rapidly in the United Kingdom to become sufficiently
   accepted that it must now be regarded as mainstream. Several factors
   explain this growth: the open data movement, research funders' and
   publishers' policies supporting data sharing, and researchers seeing
   benefits from sharing resources, including data. Another factor enabling
   qualitative data reuse has been improved services and infrastructure
   that facilitate access to thousands of data collections. The UK Data
   Service is an example of a well-established facility; more recent has
   been the proliferation of repositories being established within
   universities. This article will provide evidence of the growth of data
   reuse in the United Kingdom and in Finland by presenting both data and
   case studies of reuse that illustrate the breadth and diversity of this
   maturing research method. We use two distinct data sources that quantify
   the scale, types, and trends of reuse of qualitative data: (a) downloads
   of archived data collections held at data repositories and (b)
   publication citations. Although the focus of this article is on the
   United Kingdom, some discussion of the international environment is
   provided, together with data and examples of reuse at the Finnish Social
   Science Data Archive. The conclusion summarizes the major findings,
   including some conjectures regarding what makes qualitative data
   attractive for reuse and sharing.},
Publisher = {SAGE PUBLICATIONS INC},
Address = {2455 TELLER RD, THOUSAND OAKS, CA 91320 USA},
Type = {Article},
Language = {English},
Affiliation = {Bishop, L (Corresponding Author), Univ Essex, UK Data Arch, Colchester CO4 3SQ, Essex, England.
   Bishop, Libby, Univ Essex, UK Data Arch, Producer Relat, Colchester, Essex, England.
   Kuula-Lummi, Arja, Finnish Social Sci Data Arch, Tampere, Finland.},
DOI = {10.1177/2158244016685136},
ISSN = {2158-2440},
Keywords = {data archiving; data sharing; Finland; qualitative data; secondary
   analysis; data reuse},
Keywords-Plus = {PERSPECTIVES; REFLECTIONS},
Research-Areas = {Social Sciences - Other Topics},
Web-of-Science-Categories  = {Social Sciences, Interdisciplinary},
Author-Email = {ebishop@essex.ac.uk},
Affiliations = {University of Essex},
ORCID-Numbers = {Kuula-Luumi, Arja/0000-0003-4275-4890},
Funding-Acknowledgement = {Economic and Social Research Council {[}ES/J023477/1] Funding Source:
   researchfish; ESRC {[}ES/J023477/1] Funding Source: UKRI},
Number-of-Cited-References = {54},
Times-Cited = {76},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {28},
Journal-ISO = {SAGE Open},
Doc-Delivery-Number = {EL7CD},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000394777800020},
OA = {Green Accepted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000460119800002,
Author = {Dijkers, Marcel P.},
Title = {A beginner's guide to data stewardship and data sharing},
Journal = {SPINAL CORD},
Year = {2019},
Volume = {57},
Number = {3},
Pages = {169-182},
Month = {MAR},
Abstract = {Study design A narrative review of principles, benefits and
   disadvantages, as well as methods of research data sharing.
   Objectives To assist prospective Spinal Cord authors and others with
   understanding and implementing data sharing, so that various benefits of
   such sharing can accrue to all spinal cord injury research stakeholders.
   Setting International.
   Methods The medical research and health care services literature was
   reviewed nonsystematically for relevant articles, and web sites were
   explored for information and services offered by various pertinent
   organizations.
   Results Grant makers, professional organizations, research journals,
   publishers, and other entities in the research field increasingly stress
   the ethics as well as societal and practical benefits of data sharing,
   and require researchers to do so within a reasonable time after data
   collection ends. Sharing data, retrospectively, generally requires much
   time and resources, but when a data management plan is part of a
   research proposal from the start, costs are limited, and grant makers
   allow these costs to be part of a budget. There are many organizations
   that offer information on or even assist with preparing data for sharing
   and actual deposit in a data repository.
   Conclusions The requirement of data sharing is not likely to go away,
   and researchers interested in submitting their reports to Spinal Cord
   would do well to familiarize themselves with the myriad practical issues
   involved in preparing data for sharing.},
Publisher = {NATURE PUBLISHING GROUP},
Address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Review},
Language = {English},
Affiliation = {Dijkers, MP (Corresponding Author), Wayne State Univ, Dept Phys Med \& Rehabil, Detroit, MI 48202 USA.
   Dijkers, Marcel P., Wayne State Univ, Dept Phys Med \& Rehabil, Detroit, MI 48202 USA.},
DOI = {10.1038/s41393-018-0232-6},
ISSN = {1362-4393},
EISSN = {1476-5624},
Keywords-Plus = {OPEN ACCESS PLATFORMS; FUTURE; DESIGN; POLICY},
Research-Areas = {Neurosciences \& Neurology; Rehabilitation},
Web-of-Science-Categories  = {Clinical Neurology; Rehabilitation},
Author-Email = {marcellinus.p.dijkers@wayne.edu},
Affiliations = {Wayne State University},
Number-of-Cited-References = {70},
Times-Cited = {13},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Spinal Cord},
Doc-Delivery-Number = {HN3XZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000460119800002},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000778258200001,
Author = {Li, Yuda and Peyman, Mohammad and Panadero, Javier and Juan, Angel A.
   and Xhafa, Fatos},
Title = {IoT Analytics and Agile Optimization for Solving Dynamic Team
   Orienteering Problems with Mandatory Visits},
Journal = {MATHEMATICS},
Year = {2022},
Volume = {10},
Number = {6},
Month = {MAR},
Abstract = {Transport activities and citizen mobility have a deep impact on enlarged
   smart cities. By analyzing Big Data streams generated through Internet
   of Things (IoT) devices, this paper aims to show the efficiency of using
   IoT analytics, as an agile optimization input for solving real-time
   problems in smart cities. IoT analytics has become the main core of
   large-scale Internet applications, however, its utilization in
   optimization approaches for real-time configuration and dynamic
   conditions of a smart city has been less discussed. The challenging
   research topic is how to reach real-time IoT analytics for use in
   optimization approaches. In this paper, we consider integrating IoT
   analytics into agile optimization problems. A realistic waste collection
   problem is modeled as a dynamic team orienteering problem with mandatory
   visits. Open data repositories from smart cities are used for extracting
   the IoT analytics to achieve maximum advantage under the city
   environment condition. Our developed methodology allows us to process
   real-time information gathered from IoT systems in order to optimize the
   vehicle routing decision under dynamic changes of the traffic
   environments. A series of computational experiments is provided in order
   to illustrate our approach and discuss its effectiveness. In these
   experiments, a traditional static approach is compared against a dynamic
   one. In the former, the solution is calculated only once at the
   beginning, while in the latter, the solution is re-calculated
   periodically as new data are obtained. The results of the experiments
   clearly show that our proposed dynamic approach outperforms the static
   one in terms of rewards.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Peyman, M (Corresponding Author), Univ Oberta Catalunya, Dept Comp Sci Multimedia \& Telecommun, Barcelona 08018, Spain.
   Xhafa, F (Corresponding Author), Univ Politecn Cataluna, Dept Comp Sci, Barcelona 08034, Spain.
   Li, Yuda; Peyman, Mohammad; Panadero, Javier, Univ Oberta Catalunya, Dept Comp Sci Multimedia \& Telecommun, Barcelona 08018, Spain.
   Juan, Angel A., Univ Politecn Valencia, Dept Appl Stat \& Operat Res, Alcoy 03801, Spain.
   Xhafa, Fatos, Univ Politecn Cataluna, Dept Comp Sci, Barcelona 08034, Spain.},
DOI = {10.3390/math10060982},
Article-Number = {982},
EISSN = {2227-7390},
Keywords = {IoT analytics; big data streams; agile optimization; smart cities;
   transport analytics; dynamic team orienteering problem},
Keywords-Plus = {VEHICLE-ROUTING PROBLEM; WILLINGNESS-TO-PAY; SYSTEMS; EXTERNALITIES;
   MANAGEMENT; ALGORITHM; FRAMEWORK; LOCATION; INTERNET; SEARCH},
Research-Areas = {Mathematics},
Web-of-Science-Categories  = {Mathematics},
Author-Email = {yli1@uoc.edu
   mpeyman@uoc.edu
   jpanaderom@uoc.edu
   ajuanp@eio.upv.es
   fatos@cs.upc.edu},
Affiliations = {UOC Universitat Oberta de Catalunya; Universitat Politecnica de
   Valencia; Universitat Politecnica de Catalunya},
ResearcherID-Numbers = {Perez, Angel/HZM-0453-2023
   Juan, Angel A./GWZ-7540-2022
   Panadero, Javier/K-3496-2017
   LI, yuda/GRY-2142-2022
   },
ORCID-Numbers = {Juan, Angel A./0000-0003-1392-1776
   Panadero, Javier/0000-0002-3793-3328
   Li, Yuda/0000-0001-8031-6555
   Peyman, Mohammad/0000-0003-4734-2414},
Funding-Acknowledgement = {Ajuntament of Barcelona; Fundacio ``la Caixa{''} {[}21S09355-001]},
Funding-Text = {This project has received the support of the Ajuntament of Barcelona and
   the Fundacio ``la Caixa{''} under the framework of the Barcelona Science
   Plan 2020-2023 (grant 21S09355-001).},
Number-of-Cited-References = {67},
Times-Cited = {3},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Mathematics},
Doc-Delivery-Number = {0G7ZG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000778258200001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000381799900001,
Author = {Plis, Sergey M. and Sarwate, Anand D. and Wood, Dylan and Dieringer,
   Christopher and Landis, Drew and Reed, Cory and Panta, Sandeep R. and
   Turner, Jessica A. and Shoemaker, Jody M. and Carter, Kim W. and
   Thompson, Paul and Hutchison, Kent and Calhoun, Vince D.},
Title = {COINSTAC: A Privacy Enabled Model and Prototype for Leveraging and
   Processing Decentralized Brain Imaging Data},
Journal = {FRONTIERS IN NEUROSCIENCE},
Year = {2016},
Volume = {10},
Month = {AUG 19},
Abstract = {The field of neuroimaging has embraced the need for sharing and
   collaboration. Data sharing mandates from public funding agencies and
   major journal publishers have spurred the development of data
   repositories and neuroinformatics consortia. However, efficient and
   effective data sharing still faces several hurdles. For example, open
   data sharing is on the rise but is not suitable for sensitive data that
   are not easily shared, such as genetics. Current approaches can be
   cumbersome (such as negotiating multiple data sharing agreements). There
   are also significant data transfer, organization and computational
   challenges. Centralized repositories only partially address the issues.
   We propose a dynamic, decentralized platform for large scale analyses
   called the Collaborative Informatics and Neuroimaging Suite Toolkit for
   Anonymous Computation (COINSTAC). The COINSTAC solution can include data
   missing from central repositories, allows pooling of both open and
   ``closed{''} repositories by developing privacy-preserving versions of
   widely-used algorithms, and incorporates the tools within an easy-to-use
   platform enabling distributed computation. We present an initial
   prototype system which we demonstrate on two multi-site data sets,
   without aggregating the data. In addition, by iterating across sites,
   the COINSTAC model enables meta-analytic solutions to converge to
   ``pooled-data{''} solutions (i.e., as if the entire data were in hand).
   More advanced approaches such as feature generation, matrix
   factorization models, and preprocessing can be incorporated into such a
   model. In sum, COINSTAC enables access to the many currently unavailable
   data sets, a user friendly privacy enabled interface for decentralized
   analysis, and a powerful solution that complements existing data sharing
   solutions.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Plis, SM (Corresponding Author), Lovelace Biomed \& Environm Res Inst, Mind Res Network, Albuquerque, NM 87108 USA.
   Plis, Sergey M.; Wood, Dylan; Dieringer, Christopher; Landis, Drew; Reed, Cory; Panta, Sandeep R.; Turner, Jessica A.; Shoemaker, Jody M.; Calhoun, Vince D., Lovelace Biomed \& Environm Res Inst, Mind Res Network, Albuquerque, NM 87108 USA.
   Sarwate, Anand D., Rutgers State Univ, Dept Elect \& Comp Engn, Piscataway, NJ USA.
   Turner, Jessica A., Georgia State Univ, Dept Psychol, Univ Plaza, Atlanta, GA 30303 USA.
   Carter, Kim W., Univ Western Australia, Telethon Kids Inst, Subiaco, WA, Australia.
   Thompson, Paul, Univ Southern Calif, Imaging Genet Ctr, Enhancing Neuroimaging \& Genet Meta Anal Ctr Worl, Dept Neurol, Marina Del Rey, CA USA.
   Thompson, Paul, Univ Southern Calif, Imaging Genet Ctr, Enhancing Neuroimaging \& Genet Meta Anal Ctr Worl, Dept Psychiat, Marina Del Rey, CA USA.
   Thompson, Paul, Univ Southern Calif, Imaging Genet Ctr, Enhancing Neuroimaging \& Genet Meta Anal Ctr Worl, Dept Engn, Marina Del Rey, CA USA.
   Thompson, Paul, Univ Southern Calif, Imaging Genet Ctr, Enhancing Neuroimaging \& Genet Meta Anal Ctr Worl, Dept Radiol, Marina Del Rey, CA USA.
   Thompson, Paul, Univ Southern Calif, Imaging Genet Ctr, Enhancing Neuroimaging \& Genet Meta Anal Ctr Worl, Dept Pediat, Marina Del Rey, CA USA.
   Hutchison, Kent, Univ Colorado, Dept Psychol \& Neurosci, Boulder, CO 80309 USA.
   Calhoun, Vince D., Univ New Mexico, Dept Elect \& Comp Engn, Albuquerque, NM 87131 USA.},
DOI = {10.3389/fnins.2016.00365},
Article-Number = {365},
EISSN = {1662-453X},
Keywords = {decentralized processing; privacy; brain imaging; data sharing;
   decentralized algorithms},
Keywords-Plus = {RESTING-STATE FMRI; CHALLENGES; ALGORITHMS; DATASHIELD; PLATFORM},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Neurosciences},
Author-Email = {s.m.plis@gmail.com},
Affiliations = {Lovelace Respiratory Research Institute; Rutgers System; Rutgers New
   Brunswick; University System of Georgia; Georgia State University;
   University of Western Australia; Telethon Kids Institute; University of
   Southern California; University of Southern California; University of
   Southern California; University of Southern California; University of
   Southern California; University of Colorado System; University of
   Colorado Boulder; University of New Mexico},
ResearcherID-Numbers = {Turner, Jessica/H-7282-2015
   Calhoun, Vince D./ACN-9399-2022
   Plis, Sergey/AAA-9928-2022
   },
ORCID-Numbers = {Turner, Jessica/0000-0003-0076-8434
   Calhoun, Vince D./0000-0001-9058-0747
   Plis, Sergey/0000-0003-0040-0365
   Sarwate, Anand/0000-0001-6123-5282},
Funding-Acknowledgement = {NIH {[}1R01DA040487]; NIH BD2K program {[}U54 EB040203]; NSF
   {[}CCF-1453432]; DARPA; SSC Pacific {[}N66001-15-C-4070]; Division of
   Computing and Communication Foundations; Direct For Computer \& Info
   Scie \& Enginr {[}1453432] Funding Source: National Science Foundation},
Funding-Text = {This work was supported by the NIH under award 1R01DA040487 (to VC) and
   U54 EB040203 from the NIH BD2K program (to PT), the NSF under award
   CCF-1453432 (to AS), DARPA and SSC Pacific under contract No.
   N66001-15-C-4070 (to AS).},
Number-of-Cited-References = {86},
Times-Cited = {52},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Front. Neurosci.},
Doc-Delivery-Number = {DT9EZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000381799900001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000688480000001,
Author = {Twomey, Conal and Johnson, John A.},
Title = {Open-Source Personality Trait Norms for the United Kingdom and Ireland},
Journal = {EUROPEAN JOURNAL OF PSYCHOLOGICAL ASSESSMENT},
Year = {2022},
Volume = {38},
Number = {6},
Pages = {432-439},
Month = {NOV},
Abstract = {Most copyrighted personality inventories facilitate norm-referencing
   through illustrative tables, yet their application to the many fields
   relevant to personality measurement is constrained by the need for
   stakeholders to possess the requisite financial resources to access
   them. Using an IPIP-NEO-300 dataset from Johnson's IPIP-NEO data
   repository, we created open-source norm tables for different age groups
   (14-17 years; 18-25 years: and 30+ years) within a combined
   standardization sample from the United Kingdom (UK) and Ireland (N =
   18,591). The newly created tables are freely available online
   (https://ostio/tbmh5), and there is no need to ask for permission to
   modify them. We provide general instructions that can be used to create
   open-source personality trait norms for other countries, settings, and
   age groups, as well as gender-specific norms. There is great potential
   for these norms to be used in various settings and their open-source
   freedoms may encourage future collaborations and investigations.},
Publisher = {HOGREFE PUBLISHING CORP},
Address = {361 NEWBURY ST, 5 FL, BOSTON, MA, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Twomey, C (Corresponding Author), Ballyfermot \& Palmerstown Primary Care \& Mental H, Hlth Serv Execut, Ballyfermot Rd, Dublin 10, Ireland.
   Twomey, Conal, Ballyfermot \& Palmerstown Primary Care \& Mental H, Hlth Serv Execut, Ballyfermot Rd, Dublin 10, Ireland.
   Johnson, John A., Penn State Univ, Psychol Dept, University Pk, PA 16802 USA.},
DOI = {10.1027/1015-5759/a000644},
EarlyAccessDate = {AUG 2021},
ISSN = {1015-5759},
EISSN = {2151-2426},
Keywords = {five-factor model; International Personality Item Pool; IPIP;
   norm-referencing; open-source},
Keywords-Plus = {5 FACTOR MODEL; LIFE-SPAN; EMERGING ADULTHOOD; AGE-DIFFERENCES; OPEN
   SCIENCE; 30 FACETS; INVENTORY; BIG},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Applied},
Author-Email = {conal.twomey@hse.ie},
Affiliations = {Pennsylvania Commonwealth System of Higher Education (PCSHE);
   Pennsylvania State University; Pennsylvania State University -
   University Park},
Number-of-Cited-References = {46},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Eur. J. Psychol. Assess.},
Doc-Delivery-Number = {6Y2WP},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000688480000001},
DA = {2024-01-15},
}

@article{ WOS:000383925600005,
Author = {Morris, Devan and Wier, Megan},
Title = {Geospatially Enabled Database for Analyzing Traffic Injuries in San
   Francisco, California},
Journal = {TRANSPORTATION RESEARCH RECORD},
Year = {2016},
Number = {2595},
Pages = {40-49},
Abstract = {The collection and the analysis of transportation and health data,
   especially in geospatial terms, can be a complex process.
   TransBASESF.org is a geospatially enabled analytics database developed
   by the San Francisco, California, Department of Public Health and used
   to analyze, evaluate, monitor, and communicate transportation safety
   issues in San Francisco. The goal of TransBASESEorg is to serve as the
   central data repository for public health-related transportation data,
   to be a free and open data resource for the general public to use, and
   to support interagency collaboration, data standards, and data sharing
   in the City and County of San Francisco. The TransBASESEorg database
   currently includes more than 200 spatially referenced variables from
   multiple agencies and across a range of geographic scales, including
   infrastructure, transportation, zoning, sociodemographic, and collision
   data, all linked to an intersection or street segment. The
   TransBASESF.org database originated as a tool developed to facilitate
   health impact assessments and understand better the geographic
   distribution and characteristics of pedestrian injuries. The scope and
   the role have continued to evolve, and the database now plays a key role
   in the implementation of San Francisco's Vision Zero policy, an effort
   to reduce all modes of transportation-related fatalities to zero by
   2024. The purpose of this paper is to give an overview of the
   TransBASESF.org system, including its origin, development, content,
   technical specifications, and examples of applications to date in
   informing transportation safety planning and policy in San Francisco.},
Publisher = {NATL ACAD SCIENCES},
Address = {2101 CONSTITUTION AVE NW, WASHINGTON, DC 20418 USA},
Type = {Article},
Language = {English},
Affiliation = {Morris, D (Corresponding Author), San Francisco Dept Publ Hlth, Environm Hlth Branch, Populat Hlth Div, 1390 Market St,Suite 810, San Francisco, CA 94102 USA.
   Morris, Devan; Wier, Megan, San Francisco Dept Publ Hlth, Environm Hlth Branch, Populat Hlth Div, 1390 Market St,Suite 810, San Francisco, CA 94102 USA.},
DOI = {10.3141/2595-05},
ISSN = {0361-1981},
EISSN = {2169-4052},
Research-Areas = {Engineering; Transportation},
Web-of-Science-Categories  = {Engineering, Civil; Transportation; Transportation Science \& Technology},
Author-Email = {devan.morris@sfdph.org},
Affiliations = {San Francisco Department of Public Health},
Funding-Acknowledgement = {Centers for Disease Control and Prevention (CDC); CDC grant},
Funding-Text = {The authors acknowledge the Centers for Disease Control and Prevention
   (CDC) for funding the initial development of TransBASESF.org through a
   Health Impact Assessment to Foster Healthy Community Design grant. In
   addition, the authors thank everyone who participated and provided
   valuable insight on the technical advisory and community advisory
   committees, including their work in troubleshooting and beta testing the
   website. Cyndy Comerford helped administer the CDC grant for this
   project and provided technical guidance, and Rodell Jacinto provided
   invaluable information technology support. Finally, the authors
   specifically acknowledge the support of SFMTA staff for providing data
   for this project and institutionalizing TransBASESF.org in their own
   work.},
Number-of-Cited-References = {19},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Transp. Res. Record},
Doc-Delivery-Number = {DW8SK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000383925600005},
DA = {2024-01-15},
}

@article{ WOS:000743496700097,
Author = {Meier-Kolthoff, Jan P. and Carbasse, Joaquim Sarda and Peinado-Olarte,
   Rosa L. and Goeker, Markus},
Title = {TYGS and LPSN: a database tandem for fast and reliable genome-based
   classification and nomenclature of prokaryotes},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2022},
Volume = {50},
Number = {D1},
Pages = {D801-D807},
Month = {JAN 7},
Abstract = {Microbial systematics is heavily influenced by genome-based methods and
   challenged by an ever increasing number of taxon names and associated
   sequences in public data repositories. This poses a challenge for
   database systems, particularly since it is obviously advantageous if
   such data are based on a globally recognized approach to manage names,
   such as the International Code of Nomenclature of Prokaryotes. The
   amount of data can only be handled if accurate and reliable
   high-throughput platforms are available that are able to both comply
   with this demand and to keep track of all changes in an efficient and
   flexible way. The List of Prokaryotic names with Standing in
   Nomenclature (LPSN) is an expert-curated authoritative resource for
   prokaryotic nomenclature and is available at https://lpsn.dsmz.de. The
   Type (Strain) Genome Server (TYGS) is a high-throughput platform for
   accurate genome-based taxonomy and is available at https://tygs.dsmz.de.
   We here present important updates of these two previously introduced,
   heavily interconnected platforms for taxonomic nomenclature and
   classification, including new high-level facilities providing access to
   bioinformatic algorithms, a considerable expansion of the database
   content, and new ways to easily access the data.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Meier-Kolthoff, JP (Corresponding Author), Leibniz Inst DSMZ German Collect Microorganisms \&, Dept Bioinformat \& Databases, Inhoffenstr 7B, D-38124 Braunschweig, Germany.
   Meier-Kolthoff, Jan P.; Carbasse, Joaquim Sarda; Peinado-Olarte, Rosa L.; Goeker, Markus, Leibniz Inst DSMZ German Collect Microorganisms \&, Dept Bioinformat \& Databases, Inhoffenstr 7B, D-38124 Braunschweig, Germany.},
DOI = {10.1093/nar/gkab902},
EarlyAccessDate = {OCT 2021},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {NAMES; LIST},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {jan.meier-kolthoff@dsmz.de},
Affiliations = {Leibniz Institut fur Deutsche Sammlung von Mikroorganismen und
   Zellkulturen (DSMZ)},
ResearcherID-Numbers = {Meier-Kolthoff, Jan P./GOP-1205-2022
   },
ORCID-Numbers = {Meier-Kolthoff, Jan P./0000-0001-9105-9814
   Sarda, Joaquim/0000-0002-8417-5005},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft {[}Sonderforschungsbereich TRR 51]},
Funding-Text = {Deutsche Forschungsgemeinschaft {[}Sonderforschungsbereich TRR 51 to
   J.P.M.K.]. Funding for open access charge: Deutsche
   Forschungsgemeinschaft {[}Sonderforschungsbereich TRR 51 to J.P.M.K.].},
Number-of-Cited-References = {40},
Times-Cited = {513},
Usage-Count-Last-180-days = {10},
Usage-Count-Since-2013 = {29},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {YH9RO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000743496700097},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000949306300001,
Author = {Moolla, Iris and Hiilamo, Heikki},
Title = {Health system characteristics and COVID-19 performance in high-income
   countries},
Journal = {BMC HEALTH SERVICES RESEARCH},
Year = {2023},
Volume = {23},
Number = {1},
Month = {MAR 13},
Abstract = {BackgroundThe COVID-19 pandemic has shaken everyday life causing
   morbidity and mortality across the globe. While each country has been
   hit by the pandemic, individual countries have had different infection
   and health trajectories. Of all welfare state institutions, healthcare
   has faced the most immense pressure due to the pandemic and hence, we
   take a comparative perspective to study COVID-19 related health system
   performance. We study the way in which health system characteristics
   were associated with COVID-19 excess mortality and case fatality rates
   before Omicron variant.MethodsThis study analyses the health system
   performance during the pandemic in 43 OECD countries and selected
   non-member economies through three healthcare systems dimensions: (1)
   healthcare finance, (2) healthcare provision, (3) healthcare performance
   and health outcomes. Health system characteristics-related data is
   collected from the Global Health Observatory data repository, the
   COVID-19 related health outcome indicators from the Our World in Data
   statistics database, and the country characteristics from the World Bank
   Open Data and the OECD statistics databases.ResultsWe find that the
   COVID-19 excess mortality and case fatality rates were systematically
   associated with healthcare system financing and organizational
   structures, as well as performance regarding other health outcomes
   besides COVID-19 health outcomes.ConclusionInvestments in public health
   systems in terms of overall financing, health workforce and facilities
   are instrumental in reducing COVID-19 related mortality. Countries
   aiming at improving their pandemic preparedness may develop health
   systems by strengthening their public health systems.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Moolla, I (Corresponding Author), Univ Helsinki, Dept Social Res, Helsinki, Finland.
   Moolla, Iris; Hiilamo, Heikki, Univ Helsinki, Dept Social Res, Helsinki, Finland.},
DOI = {10.1186/s12913-023-09206-z},
Article-Number = {244},
EISSN = {1472-6963},
Keywords = {Healthcare performance; COVID-19 pandemic; Health system structures;
   Healthcare financing; Healthcare provision and organization; Health
   outcomes},
Keywords-Plus = {POPULATION HEALTH; WELFARE REGIMES; HUMAN-RESOURCES; CARE-SYSTEMS;
   MORTALITY; OUTCOMES; POLITICS; IMPACT},
Research-Areas = {Health Care Sciences \& Services},
Web-of-Science-Categories  = {Health Care Sciences \& Services},
Author-Email = {iris.moolla@helsinki.fi},
Affiliations = {University of Helsinki},
Number-of-Cited-References = {63},
Times-Cited = {2},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {6},
Journal-ISO = {BMC Health Serv. Res.},
Doc-Delivery-Number = {9W8DP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000949306300001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000374090200001,
Author = {Reiser, Leonore and Berardini, Tanya Z. and Li, Donghui and Muller,
   Robert and Strait, Emily M. and Li, Qian and Mezheritsky, Yarik and
   Vetushko, Andrey and Huala, Eva},
Title = {Sustainable funding for biocuration: The Arabidopsis Information
   Resource (TAIR) as a case study of a subscription-based funding model},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2016},
Month = {MAR 17},
Abstract = {Databases and data repositories provide essential functions for the
   research community by integrating, curating, archiving and otherwise
   packaging data to facilitate discovery and reuse. Despite their
   importance, funding for maintenance of these resources is increasingly
   hard to obtain. Fueled by a desire to find long term, sustainable
   solutions to database funding, staff from the Arabidopsis Information
   Resource (TAIR), founded the nonprofit organization, Phoenix
   Bioinformatics, using TAIR as a test case for user-based funding.
   Subscription-based funding has been proposed as an alternative to grant
   funding but its application has been very limited within the nonprofit
   sector. Our testing of this model indicates that it is a viable option,
   at least for some databases, and that it is possible to strike a balance
   that maximizes access while still incentivizing subscriptions. One year
   after transitioning to subscription support, TAIR is self-sustaining and
   Phoenix is poised to expand and support additional resources that wish
   to incorporate user-based funding strategies.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Huala, E (Corresponding Author), Phoenix Bioinformat, Arabidopsis Informat Resource, 643 Bair Isl Rd Suite 403, Redwood City, CA 94063 USA.
   Reiser, Leonore; Berardini, Tanya Z.; Li, Donghui; Muller, Robert; Strait, Emily M.; Li, Qian; Mezheritsky, Yarik; Vetushko, Andrey; Huala, Eva, Phoenix Bioinformat, Arabidopsis Informat Resource, 643 Bair Isl Rd Suite 403, Redwood City, CA 94063 USA.},
DOI = {10.1093/database/baw018},
Article-Number = {baw018},
ISSN = {1758-0463},
Keywords-Plus = {DATABASE; GENOME; IDENTIFICATION; ANNOTATION},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {huala@phoenixbioinformatics.org},
ResearcherID-Numbers = {Huala, Eva L/B-1377-2009
   },
ORCID-Numbers = {Berardini, Tanya/0000-0002-3837-8864
   Reiser, Leonore/0000-0003-0073-0858
   Huala, Eva/0000-0003-4631-7241
   Li, Donghui/0000-0003-3335-4537},
Funding-Acknowledgement = {Sloan Foundation; National Human Genome Research Institute of the
   National Institutes of Health {[}5U41HG002273-14]},
Funding-Text = {This work was funded by national, academic institutional, corporate and
   individual subscriptions to TAIR and a grant from the Sloan Foundation.
   Open access publication is funded by subscriptions. GO work at TAIR is
   funded by a subcontract on a grant from the National Human Genome
   Research Institute of the National Institutes of Health to the GO
   Consortium 5U41HG002273-14.},
Number-of-Cited-References = {35},
Times-Cited = {27},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Database},
Doc-Delivery-Number = {DJ3FM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000374090200001},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000792911200003,
Author = {Free, Christopher M. and Poulsen, Camila Vargas and Bellquist, Lyall F.
   and Wassermann, Sophia N. and Oken, Kiva L.},
Title = {The CALFISH database: A century of California's non-confidential
   fisheries landings and participation data},
Journal = {ECOLOGICAL INFORMATICS},
Year = {2022},
Volume = {69},
Month = {JUL},
Abstract = {California's commercial and recreational fisheries support vibrant
   coastal economies and communities. Maintaining healthy fishing
   communities into the future requires a detailed understanding of their
   past. The California Department of Fish and Wildlife (CDFW) has been
   monitoring statewide fisheries landings and participation since 1916 and
   releases confidential versions of this data through authorized data
   requests and non-confidential summaries of this data in its quasi-annual
   landings reports. The non-confidential data published in the landings
   reports provide a rich history of California's fisheries but are
   scattered across 1000s of tables in 100 s of documents, limiting their
   accessibility to researchers, fishers, and other interested
   stakeholders. We reviewed the 58 landings reports published from 1929 to
   2020 and extracted and carefully curated 13 datasets with long time
   series and wide public interest. These datasets include: (1) annual
   landings in pounds and value by port and species from 1941 to 2019; (2)
   annual number of commercial fishing vessels by length class from 1934 to
   2020; (3) annual number of licensed commercial fishers by area of
   residence from 1916 to 2020; and (4) annual number of party boat (CPFV)
   vessels, anglers, and their total catch by species from 1936 to 2020.
   Notably, we harmonized port names, species common names, and species
   scientific names across all years and datasets. We make these curated
   datasets, collectively called the CALFISH database, publicly available
   to any interested stakeholder in the supplementary materials of this
   paper, on an open-access data-repository, and in the wcfish R package.
   These datasets can be used (1) to understand the historical context of
   California's fisheries; (2) for original research requiring only
   summaries of historical landings and participation data; and (3) to
   anticipate the likely characteristics of confidential data requested
   from the state. We conclude the paper by identifying key principles for
   increasing the accessibility and utility of historical fisheries
   landings and participation data.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Free, CM (Corresponding Author), Univ Calif Santa Barbara, Bren Sch Environm Sci \& Management, 2400 Bren Hall, Santa Barbara, CA 93106 USA.
   Free, Christopher M.; Poulsen, Camila Vargas, Univ Calif Santa Barbara, Bren Sch Environm Sci \& Management, 2400 Bren Hall, Santa Barbara, CA 93106 USA.
   Free, Christopher M., Univ Calif Santa Barbara, Marine Sci Inst, Santa Barbara, CA 93106 USA.
   Bellquist, Lyall F., Nature Conservancy, Calif Oceans Program, San Francisco, CA 94105 USA.
   Bellquist, Lyall F., Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA.
   Wassermann, Sophia N., Univ Washington, Sch Aquat \& Fisheries Sci, Seattle, WA 98195 USA.
   Oken, Kiva L., Northwest Fisheries Sci Ctr, Fishery Resource Anal \& Monitoring Div, Seattle, WA 98112 USA.},
DOI = {10.1016/j.ecoinf.2022.101599},
EarlyAccessDate = {FEB 2022},
Article-Number = {101599},
ISSN = {1574-9541},
EISSN = {1878-0512},
Keywords = {Commercial fisheries; Recreational fisheries; Marine fisheries; Catch;
   Fishing fleets; Fishing ports},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {cfree@ucsb.edu},
Affiliations = {University of California System; University of California Santa Barbara;
   University of California System; University of California Santa Barbara;
   Nature Conservancy; University of California System; University of
   California San Diego; Scripps Institution of Oceanography; University of
   Washington; University of Washington Seattle},
ResearcherID-Numbers = {Free, Christopher Michael/AAC-5103-2019
   },
ORCID-Numbers = {Free, Christopher Michael/0000-0002-2557-8920
   Bellquist, Lyall/0000-0003-1247-0483
   Wassermann, Sophia Nell/0000-0002-4323-5227},
Funding-Acknowledgement = {The Nature Conservancy; NOAA {[}NA18OAR4170073]; California Sea Grant
   College Program Project, through NOAA'S National Sea Grant College
   Program, U.S. Dept. of Commerce {[}R/SFA-09]},
Funding-Text = {We are grateful to the fishers, processors, dealers, port samplers,
   biologists, and other CDFW employees that contribute to the collection,
   curation, and publication of data on California's fisheries. We thank
   Paulo Serpa, Joann Eres, and Todd Neahr for their guidance on the CDFW
   data and Alexis Jackson, Kate Kauer, and the TNC CA Oceans Program for
   feedback on the manuscript. C.F. and C.V.P were supported through
   funding from The Nature Conservancy. S.N.W. was supported by NOAA Grant
   \#NA18OAR4170073, California Sea Grant College Program Project
   \#R/SFA-09, through NOAA'S National Sea Grant College Program, U.S.
   Dept. of Commerce. The statements, findings, conclusions and
   recommendations are those of the author(s) and do not necessarily
   reflect the views of California Sea Grant, NOAA or the U.S. Dept. of
   Commerce.},
Number-of-Cited-References = {72},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Ecol. Inform.},
Doc-Delivery-Number = {1C1TW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000792911200003},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000312893300097,
Author = {Felder, Marius and Romualdi, Alessandro and Petzold, Andreas and
   Platzer, Matthias and Suehnel, Juergen and Gloeckner, Gernot},
Title = {GenColors-based comparative genome databases for small eukaryotic
   genomes},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2013},
Volume = {41},
Number = {D1},
Pages = {D692-D699},
Month = {JAN},
Abstract = {Many sequence data repositories can give a quick and easily accessible
   overview on genomes and their annotations. Less widespread is the
   possibility to compare related genomes with each other in a common
   database environment. We have previously described the GenColors
   database system (http://gencolors.fli-leibniz.de) and its applications
   to a number of bacterial genomes such as Borrelia, Legionella,
   Leptospira and Treponema. This system has an emphasis on genome
   comparison. It combines data from related genomes and provides the user
   with an extensive set of visualization and analysis tools. Eukaryote
   genomes are normally larger than prokaryote genomes and thus pose
   additional challenges for such a system. We have, therefore, adapted
   GenColors to also handle larger datasets of small eukaryotic genomes and
   to display eukaryotic gene structures. Further recent developments
   include whole genome views, genome list options and, for bacterial
   genome browsers, the display of horizontal gene transfer predictions.
   Two new GenColors-based databases for two fungal species
   (http://fgb.fli-leibniz.de) and for four social amoebas
   (http://sacgb.fli-leibniz.de) were set up. Both new resources open up a
   single entry point for related genomes for the amoebozoa and fungal
   research communities and other interested users. Comparative genomics
   approaches are greatly facilitated by these resources.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Felder, M (Corresponding Author), Fritz Lipmann Inst, Leibniz Inst Age Res, Genome Anal Grp, Beutenbergstr 11, D-07745 Jena, Germany.
   Felder, Marius; Petzold, Andreas; Platzer, Matthias, Fritz Lipmann Inst, Leibniz Inst Age Res, Genome Anal Grp, D-07745 Jena, Germany.
   Romualdi, Alessandro, Univ Klinikum Jena, D-07747 Jena, Germany.
   Suehnel, Juergen, Fritz Lipmann Inst, Leibniz Inst Age Res, Biocomp Grp, D-07745 Jena, Germany.
   Gloeckner, Gernot, Univ Cologne, Fac Med, Inst Biochem 1, D-50931 Cologne, Germany.
   Gloeckner, Gernot, Leibniz Inst Freshwater Ecol \& Inland Fisheries, Mol Biol Grp, D-12587 Berlin, Germany.},
DOI = {10.1093/nar/gks1176},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PROKARYOTIC GENOMES; ANNOTATION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {mfelder@fli-leibniz.de},
Affiliations = {Leibniz Institut fur Alternsforschung - Fritz-Lipmann-Institut (FLI);
   Friedrich Schiller University of Jena; Leibniz Institut fur
   Alternsforschung - Fritz-Lipmann-Institut (FLI); University of Cologne;
   Leibniz Institut fur Gewasserokologie und Binnenfischerei (IGB)},
ResearcherID-Numbers = {Glöckner, Gernot/A-7800-2010},
ORCID-Numbers = {Glöckner, Gernot/0000-0002-9061-1061},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft (DFG) {[}Gl235/1-2]; Leibniz Institute
   for Age Research - Fritz Lipmann Institute},
Funding-Text = {Deutsche Forschungsgemeinschaft (DFG; Gl235/1-2). Funding for open
   access charge: Leibniz Institute for Age Research - Fritz Lipmann
   Institute.},
Number-of-Cited-References = {24},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {14},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {062BE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000312893300097},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000312893300140,
Author = {Rustici, Gabriella and Kolesnikov, Nikolay and Brandizi, Marco and
   Burdett, Tony and Dylag, Miroslaw and Emam, Ibrahim and Farne, Anna and
   Hastings, Emma and Ison, Jon and Keays, Maria and Kurbatova, Natalja and
   Malone, James and Mani, Roby and Mupo, Annalisa and Pereira, Rui Pedro
   and Pilicheva, Ekaterina and Rung, Johan and Sharma, Anjan and Tang, Y.
   Amy and Ternent, Tobias and Tikhonov, Andrew and Welter, Danielle and
   Williams, Eleanor and Brazma, Alvis and Parkinson, Helen and Sarkans,
   Ugis},
Title = {ArrayExpress update-trends in database growth and links to data analysis
   tools},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2013},
Volume = {41},
Number = {D1},
Pages = {D987-D990},
Month = {JAN},
Abstract = {The ArrayExpress Archive of Functional Genomics Data
   (http://www.ebi.ac.uk/arrayexpress) is one of three international
   functional genomics public data repositories, alongside the Gene
   Expression Omnibus at NCBI and the DDBJ Omics Archive, supporting
   peer-reviewed publications. It accepts data generated by sequencing or
   array-based technologies and currently contains data from almost a
   million assays, from over 30 000 experiments. The proportion of
   sequencing-based submissions has grown significantly over the last 2
   years and has reached, in 2012, 15\% of all new data. All data are
   available from ArrayExpress in MAGE-TAB format, which allows robust
   linking to data analysis and visualization tools, including Bioconductor
   and GenomeSpace. Additionally, R objects, for microarray data, and
   binary alignment format files, for sequencing data, have been generated
   for a significant proportion of ArrayExpress data.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Rustici, G (Corresponding Author), EMBL EBI, Funct Genom Team, Wellcome Trust Genome Campus, Hinxton CB10 1SD, England.
   Rustici, Gabriella; Kolesnikov, Nikolay; Brandizi, Marco; Burdett, Tony; Dylag, Miroslaw; Emam, Ibrahim; Hastings, Emma; Ison, Jon; Keays, Maria; Kurbatova, Natalja; Malone, James; Mani, Roby; Pereira, Rui Pedro; Pilicheva, Ekaterina; Rung, Johan; Sharma, Anjan; Tang, Y. Amy; Ternent, Tobias; Tikhonov, Andrew; Welter, Danielle; Williams, Eleanor; Brazma, Alvis; Parkinson, Helen; Sarkans, Ugis, EMBL EBI, Funct Genom Team, Hinxton CB10 1SD, England.
   Farne, Anna; Mupo, Annalisa, Wellcome Trust Sanger Inst, Hinxton CB10 1SA, England.},
DOI = {10.1093/nar/gks1174},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MICROARRAY DATA; FORMAT; BIOINFORMATICS; MIAME},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {gabry@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL); Wellcome Trust Sanger
   Institute},
ResearcherID-Numbers = {Brandizi, Marco/X-6605-2019
   Williams, Eleanor/JKJ-6665-2023
   },
ORCID-Numbers = {Brandizi, Marco/0000-0002-5427-2496
   Keays, Maria/0000-0003-2034-601X
   Rustici, Gabriella/0000-0003-3085-1271
   Williams, Eleanor/0000-0002-0851-7990
   Hastings, Emma/0000-0001-9927-8560
   Ison, Jon/0000-0001-6666-1520
   Burdett, Anthony/0000-0002-2513-5396
   Welter, Danielle/0000-0003-1058-2668
   Brazma, Alvis/0000-0001-5988-7409
   Kurbatova, Natalja/0000-0002-3973-2909
   Sarkans, Ugis/0000-0001-9227-8488
   Mupo, Annalisa/0000-0002-2771-0462
   Rung, Johan/0000-0001-5875-8429
   Kolesnikov, Nikolay/0000-0001-7139-7103
   Parkinson, Helen/0000-0003-3035-4195
   Tang, Amy/0000-0003-0045-1234
   Malone, James Robert/0000-0002-1615-2899
   Emam, Ibrahim/0000-0002-7561-2787
   Ternent, Tobias/0000-0003-0279-7335},
Funding-Acknowledgement = {European Molecular Biology Laboratory; European Commission {[}201413,
   260791, 261123, 226073, 242220, 200754]; US National Institutes of
   Health (the National Human Genome Research Institute) {[}P41 HG003619];
   US National Institutes of Health (National Institute of Biomedical
   Imaging and Bioengineering) {[}P41 HG003619]; US National Institutes of
   Health (National Cancer Institute) {[}P41 HG003619]; National Center for
   Biomedical Ontology, one of the National Centers for Biomedical
   Computing; National Human Genome Research Institute, the National Heart,
   Lung, and Blood Institute, and National Institutes of Health Common Fund
   {[}U54-HG004028]; National Science Foundation {[}1127112]; EMBL; BBSRC
   {[}BB/E001653/1] Funding Source: UKRI; Biotechnology and Biological
   Sciences Research Council {[}BB/E001653/1] Funding Source: researchfish},
Funding-Text = {ArrayExpress and related activities are supported by member states of
   the European Molecular Biology Laboratory; European Commission: ENGAGE
   {[}201413], EurocanPlatform {[}260791], GEUVADIS {[}261123], SLING
   {[}226073], SYBARIS {[}242220], and Gen2Phen {[}200754]; US National
   Institutes of Health (the National Human Genome Research Institute,
   National Institute of Biomedical Imaging and Bioengineering and the
   National Cancer Institute) {[}P41 HG003619]; National Center for
   Biomedical Ontology, one of the National Centers for Biomedical
   Computing supported by the National Human Genome Research Institute, the
   National Heart, Lung, and Blood Institute, and National Institutes of
   Health Common Fund {[}U54-HG004028]; National Science Foundation Award
   Number {[}1127112]. Funding for open access charge: EMBL Members states.},
Number-of-Cited-References = {20},
Times-Cited = {282},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {21},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {062BE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000312893300140},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000304923700006,
Author = {Vasilevsky, Nicole and Johnson, Tenille and Corday, Karen and Torniai,
   Carlo and Brush, Matthew and Segerdell, Erik and Wilson, Melanie and
   Shaffer, Chris and Robinson, David and Haendel, Melissa},
Title = {Research resources: curating the new eagle-i discovery system},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2012},
Month = {MAR 20},
Abstract = {Development of biocuration processes and guidelines for new data types
   or projects is a challenging task. Each project finds its way toward
   defining annotation standards and ensuring data consistency with varying
   degrees of planning and different tools to support and/or report on
   consistency. Further, this process may be data type specific even within
   the context of a single project. This article describes our experiences
   with eagle-i, a 2-year pilot project to develop a federated network of
   data repositories in which unpublished, unshared or otherwise
   `invisible' scientific resources could be inventoried and made
   accessible to the scientific community. During the course of eagle-i
   development, the main challenges we experienced related to the
   difficulty of collecting and curating data while the system and the data
   model were simultaneously built, and a deficiency and diversity of data
   management strategies in the laboratories from which the source data was
   obtained. We discuss our approach to biocuration and the importance of
   improving information management strategies to the research process,
   specifically with regard to the inventorying and usage of research
   resources. Finally, we highlight the commonalities and differences
   between eagle-i and similar efforts with the hope that our lessons
   learned will assist other biocuration endeavors.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Haendel, M (Corresponding Author), Oregon Hlth \& Sci Univ, LIB, 3181 SW Sam Jackson Pk Rd, Portland, OR 97239 USA.
   Vasilevsky, Nicole; Torniai, Carlo; Brush, Matthew; Segerdell, Erik; Wilson, Melanie; Shaffer, Chris; Robinson, David; Haendel, Melissa, Oregon Hlth \& Sci Univ, LIB, Portland, OR 97239 USA.
   Johnson, Tenille; Corday, Karen, Harvard Univ, Sch Med, Ctr Biomed Informat, Boston, MA 02139 USA.},
DOI = {10.1093/database/bar067},
Article-Number = {bar067},
ISSN = {1758-0463},
Keywords-Plus = {INTEGRATION; GUIDELINES; FUTURE},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {haendel@ohsu.edu},
Affiliations = {Oregon Health \& Science University; Harvard University; Harvard Medical
   School},
ResearcherID-Numbers = {Vasilevsky, Nicole A/AAB-7589-2019
   },
ORCID-Numbers = {Vasilevsky, Nicole A/0000-0001-5208-3432
   Segerdell, Erik/0000-0002-9611-1279
   Haendel, Melissa/0000-0001-9114-8737
   Robinson, David/0000-0003-2399-0679},
Funding-Acknowledgement = {National Institutes of Health; American Recovery and Reinvestment Act
   {[}1U24RR029825-01]},
Funding-Text = {Funding for open access charge: The National Institutes of Health and
   the American Recovery and Reinvestment Act (1U24RR029825-01).},
Number-of-Cited-References = {22},
Times-Cited = {21},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Database},
Doc-Delivery-Number = {954CL},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000304923700006},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:001011745100006,
Author = {Santesteban, Luis Gonzaga and Rekarte, Isabel and Torres, Nazareth and
   Villa-Llop, Ana and Visconti, Fernando and Intrigliolo, Diego S. and
   Escalona, Jose M. and de Herralde, Felicidad and Miranda, Carlos},
Title = {The role of rootstocks for grape growing adaptation to climate change.
   Meta-analysis of the research conducted in Spanish viticulture},
Journal = {OENO ONE},
Year = {2023},
Volume = {57},
Number = {2},
Pages = {283-290},
Abstract = {Rootstock election is one of the key decisions when designing a
   vineyard. Although the research performed to determine the effect they
   induce in the behaviour of scion varieties is not scarce, it is not easy
   to have a global idea, as results are usually published scattered. In
   this work, we re-examine previous research conducted in Spain on
   rootstock implications on vine agronomic performance through the
   performance of a meta-analysis (MA). As a result, we were able to
   integrate the information reported in 20 articles that included
   rootstock experimentation conducted with 36 different varieties and 47
   different rootstocks, totalling 764 individual records. However, when
   the information was filtered before the meta-analysis, this number
   decreased to 312 records, for which rootstock Response Ratios (RR) were
   calculated. The characteristics conferred by the rootstock were more
   closely related to the rootstock itself, rather than to the
   characteristics of the Vitis sp. crossing used to create the rootstock.
   Several rootstocks were identified as more suitable for adapting to
   future climate change conditions, as far as they were able to moderate
   sugar accumulation and pH (161-49 C, 41-B MGt and 420A MGt). Meanwhile,
   140 Ru and 5-BB were observed to provide high pH and sugar contents
   despite their high yield. In conclusion, despite being based on data
   from a single country, the meta-analysis was shown to be a useful tool
   for enhancing the value of previous research on rootstocks. Combining
   articles from both peer-reviewed and technical journals helped in the
   assessment of the implications of different rootstocks, although further
   steps should be taken to facilitate data integration (harmonisation of
   measurement and reporting procedures, open data repositories, etc).},
Publisher = {INT VITICULTURE \& ENOLOGY SOC-IVES},
Address = {INST SCI VIGNE VIN-ISVV, 210 CHEMIN DE LEYSOTTE, VILLENAVE D ORNON,
   FRANCE},
Type = {Article},
Language = {English},
Affiliation = {Santesteban, LG (Corresponding Author), Publ Univ Navarre UPNA, Dept Agron Biotechnol \& Food, Campus Arrosadia, Pamplona, Spain.
   Santesteban, LG (Corresponding Author), Inst Multidisciplinary Res Appl Biol IMAB, Pamplona, Spain.
   Santesteban, Luis Gonzaga; Rekarte, Isabel; Torres, Nazareth; Villa-Llop, Ana; Miranda, Carlos, Publ Univ Navarre UPNA, Dept Agron Biotechnol \& Food, Campus Arrosadia, Pamplona, Spain.
   Santesteban, Luis Gonzaga; Torres, Nazareth; Miranda, Carlos, Inst Multidisciplinary Res Appl Biol IMAB, Pamplona, Spain.
   Villa-Llop, Ana, Vitis Navarra Nursery, Larraga, Spain.
   Visconti, Fernando; Intrigliolo, Diego S., UVEG, CSIC, Desertificat Res Ctr CIDE, GVA, Valencia, Spain.
   Escalona, Jose M., Univ Balearic Isl UIB, Dept Biol, Palma De Mallorca, Spain.
   Escalona, Jose M., Univ Balearic Isl INAGEA UIB, Agroenvironm \& Water Econ Inst, Plant Biol \& Environm, Palma De Mallorca, Spain.
   de Herralde, Felicidad, Inst Recerca \& Tecnol Agroalimentaries IRTA, Torre Marimon, Barcelona, Spain.},
DOI = {10.20870/oeno-one.2023.57.2.7439},
EISSN = {2494-1271},
Keywords = {meta-analysis; rootstock; yield; vegetative development; grape
   composition; climate change},
Keywords-Plus = {BIODIVERSITY},
Research-Areas = {Food Science \& Technology},
Web-of-Science-Categories  = {Food Science \& Technology},
Author-Email = {gonzaga.santesteban@unavarra.es},
Affiliations = {Universidad Publica de Navarra; Consejo Superior de Investigaciones
   Cientificas (CSIC); University of Valencia; CSIC-GV-UV - Centro de
   Investigaciones sobre Desertificacion (CIDE); Universitat de les Illes
   Balears; IRTA},
ResearcherID-Numbers = {de Herralde, Felicidad/A-2817-2014
   Miranda, Carlos/B-4293-2010
   Santesteban, Luis Gonzaga/B-2408-2009
   },
ORCID-Numbers = {de Herralde, Felicidad/0000-0003-1274-1482
   Miranda, Carlos/0000-0001-7217-0859
   Santesteban, Luis Gonzaga/0000-0001-6924-6744
   escalona, jose/0000-0002-6764-798X
   Visconti, Fernando/0000-0003-4393-0972},
Funding-Acknowledgement = {MCIN/AEI {[}PDC2021-121210-C21, PDC2021-121210-C22,
   PID2021-123305OB-C32]; European Union NextGenerationEU/PRTR},
Funding-Text = {This work has been carried out within the context of the WANUGRAPE 4.0
   project (grant nos. PDC2021-121210-C21 and PDC2021-121210-C22) and
   UPGRAPE PID2021-123305OB-C32, funded by MCIN/AEI/10.13039/501100011033
   and by the ``European Union NextGenerationEU/PRTR{''}\& nbsp;},
Number-of-Cited-References = {21},
Times-Cited = {0},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {8},
Journal-ISO = {OENE One},
Doc-Delivery-Number = {J7YP1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001011745100006},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:001026459400001,
Author = {Fakiris, Elias and Dimas, Xenophon and Giannakopoulos, Vasileios and
   Geraga, Maria and Koutsikopoulos, Constantin and Ferentinos, George and
   Papatheodorou, George},
Title = {Improved predictive modelling of coralligenous formations in the Greek
   Seas incorporating large-scale, presence-absence, hydroacoustic data and
   oceanographic variables},
Journal = {FRONTIERS IN MARINE SCIENCE},
Year = {2023},
Volume = {10},
Month = {JUN 28},
Abstract = {Our understanding of the distribution of coralligenous formations,
   throughout but mostly on the Eastern Mediterranean seafloor, is still
   poor and mostly relies on presence-only opportunistic trawling and
   fishermen reports. Previous efforts to gather this information created
   relevant geodatabases that led to a first draft predictive spatial
   distribution of coralligenous formations in the Mediterranean Sea using
   habitat suitability modelling techniques. In the last few decades, the
   use of hydroacoustics to map the seafloor for various geotechnical and
   habitat mapping projects accumulated high amounts of detailed spatial
   information about these formations, which remains majorly unexploited.
   Repurposing these datasets towards mapping key habitats is a valuable
   stepping stone to implementing the EU Habitat Directive. In Greece, a
   unique volume of seafloor mapping data has been gathered by the
   Laboratory of Marine Geology and Physical Oceanography, Geology
   Department, University of Patras. It accounts for more than 33 marine
   geophysical expeditions during the last three decades, having collected
   hydroacoustic data for a total seafloor area of 3,197.68 km(2). In the
   present work, this information has been curated, re-evaluated, and
   archived to create the most complete, until now, atlas of coralligenous
   formations in the Greek Seas and the only integrating presence-absence
   data. This atlas has been used to train and validate a predictive
   distribution model, incorporating environmental variables derived from
   open data repositories, whose importance has been assessed and
   discussed. The final output is an improved probability map of
   coralligenous formation occurrence in the Greek Seas, which shall be the
   basis for effective spatial planning, gap detection, and design of
   future mapping and monitoring activities on this priority habitat.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Papatheodorou, G (Corresponding Author), Univ Patras, Dept Geol, Lab Marine Geol \& Phys Oceanog, Rion, Greece.
   Fakiris, Elias; Dimas, Xenophon; Giannakopoulos, Vasileios; Geraga, Maria; Ferentinos, George; Papatheodorou, George, Univ Patras, Dept Geol, Lab Marine Geol \& Phys Oceanog, Rion, Greece.
   Koutsikopoulos, Constantin, Univ Patras, Dept Biol, Rion, Greece.},
DOI = {10.3389/fmars.2023.1117919},
Article-Number = {1117919},
EISSN = {2296-7745},
Keywords = {predictive distribution modelling; habitat mapping; bioconstructions;
   Mediterranean; sidescan sonar},
Keywords-Plus = {BENTHIC HABITAT; RANDOM FORESTS; CORAL-REEFS; WATER; CLASSIFICATION;
   RHODOLITHS; PHOTOSYNTHESIS; SUBSTRATUM; COMMUNITY; SIDESCAN},
Research-Areas = {Environmental Sciences \& Ecology; Marine \& Freshwater Biology},
Web-of-Science-Categories  = {Environmental Sciences; Marine \& Freshwater Biology},
Author-Email = {gpapathe@upatras.gr},
Affiliations = {University of Patras; University of Patras},
ORCID-Numbers = {Giannakopoulos, Vasileios/0000-0003-0861-654X},
Funding-Acknowledgement = {European Union (European Social Fund-ESF) through the Operational
   Programme ``Human Resources Development, Education and Lifelong
   Learning{''} in the context of the project ``Reinforcement of
   Postdoctoral Researchers-2nd Cycle{''} {[}MIS-5033021]; Research Council
   of the University of Patras},
Funding-Text = {This research is co-financed by Greece and the European Union (European
   Social Fund-ESF) through the Operational Programme ``Human Resources
   Development, Education and Lifelong Learning{''} in the context of the
   project ``Reinforcement of Postdoctoral Researchers-2nd Cycle{''}
   (MIS-5033021), implemented by the State Scholarships Foundation (IKY).
   Data acquisition and interpretation are a cumulative effort of more than
   34 unclassified academic and commercial projects of Oceanus-Lab,
   spanning 31 years of research. The publication fees of this manuscript
   have been financed by the Research Council of the University of Patras.},
Number-of-Cited-References = {71},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Front. Mar. Sci.},
Doc-Delivery-Number = {L9NK3},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001026459400001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000276399100074,
Author = {Harris, Todd W. and Antoshechkin, Igor and Bieri, Tamberlyn and Blasiar,
   Darin and Chan, Juancarlos and Chen, Wen J. and De La Cruz, Norie and
   Davis, Paul and Duesbury, Margaret and Fang, Ruihua and Fernandes,
   Jolene and Han, Michael and Kishore, Ranjana and Lee, Raymond and
   Mueller, Hans-Michael and Nakamura, Cecilia and Ozersky, Philip and
   Petcherski, Andrei and Rangarajan, Arun and Rogers, Anthony and
   Schindelman, Gary and Schwarz, Erich M. and Tuli, Mary Ann and Van
   Auken, Kimberly and Wang, Daniel and Wang, Xiaodong and Williams, Gary
   and Yook, Karen and Durbin, Richard and Stein, Lincoln D. and Spieth,
   John and Sternberg, Paul W.},
Title = {WormBase: a comprehensive resource for nematode research},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2010},
Volume = {38},
Number = {1},
Pages = {D463-D467},
Month = {JAN},
Abstract = {WormBase (http://www.wormbase.org) is a central data repository for
   nematode biology. Initially created as a service to the Caenorhabditis
   elegans research field, WormBase has evolved into a powerful research
   tool in its own right. In the past 2 years, we expanded WormBase to
   include the complete genomic sequence, gene predictions and orthology
   assignments from a range of related nematodes. This comparative data
   enrich the C. elegans data with improved gene predictions and a better
   understanding of gene function. In turn, they bring the wealth of
   experimental knowledge of C. elegans to other systems of medical and
   agricultural importance. Here, we describe new species and data types
   now available at WormBase. In addition, we detail enhancements to our
   curatorial pipeline and website infrastructure to accommodate new
   genomes and an extensive user base.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Harris, TW (Corresponding Author), Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada.
   Harris, Todd W.; De La Cruz, Norie; Stein, Lincoln D., Ontario Inst Canc Res, Toronto, ON M5G 0A3, Canada.
   Antoshechkin, Igor; Chan, Juancarlos; Chen, Wen J.; Fang, Ruihua; Fernandes, Jolene; Kishore, Ranjana; Lee, Raymond; Mueller, Hans-Michael; Nakamura, Cecilia; Petcherski, Andrei; Rangarajan, Arun; Schindelman, Gary; Schwarz, Erich M.; Tuli, Mary Ann; Van Auken, Kimberly; Wang, Daniel; Wang, Xiaodong; Yook, Karen; Sternberg, Paul W., CALTECH, Div Biol, Pasadena, CA 91125 USA.
   Bieri, Tamberlyn; Blasiar, Darin; Ozersky, Philip; Spieth, John, Washington Univ, Sch Med, Genome Sequencing Ctr, St Louis, MO 63108 USA.
   Sternberg, Paul W., CALTECH, Howard Hughes Med Inst, Pasadena, CA 91125 USA.},
DOI = {10.1093/nar/gkp952},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENOME; PARASITISM; PATHWAYS; SEQUENCE; DATABASE; ELEGANS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {info@toddharris.net},
Affiliations = {Ontario Institute for Cancer Research; University of Toronto; California
   Institute of Technology; Washington University (WUSTL); California
   Institute of Technology; Howard Hughes Medical Institute},
ResearcherID-Numbers = {chen, wenjing/IZE-8536-2023
   Durbin, Richard/AAE-7178-2019
   Paulini, Michael/E-8289-2017
   Muller, Hans-Michael/J-9624-2015
   Tuli, Mary Ann/AAI-7829-2020
   },
ORCID-Numbers = {Durbin, Richard/0000-0002-9130-1006
   Paulini, Michael/0000-0002-6968-2340
   Tuli, Mary Ann/0000-0002-4667-9528
   Duesbury, Margaret/0000-0002-4904-1247
   Schwarz, Erich/0000-0003-3151-4381
   Yook, Karen/0000-0002-4457-6787
   Davis, Paul/0000-0001-5545-0824
   Harris, Todd/0000-0003-3406-163X
   Sternberg, Paul/0000-0002-7699-0173},
Funding-Acknowledgement = {US National Institutes of Health {[}P41 HG02223]; US National Human
   Genome Research Institute {[}P41-HG02223]; British Medical Research
   Council; Medical Research Council {[}G0701197] Funding Source:
   researchfish; MRC {[}G0701197] Funding Source: UKRI},
Funding-Text = {US National Institutes of Health (Grant no. P41 HG02223); US National
   Human Genome Research Institute (Grant no. P41-HG02223 to WormBase);
   British Medical Research Council (to WormBase); P. W. S. is an
   investigator with the Howard Hughes Medical Institute. Funding for open
   access charge: US National Human Genome Research Institute (Grant P41-
   HG02223).},
Number-of-Cited-References = {23},
Times-Cited = {273},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {18},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {579TV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000276399100074},
OA = {Green Submitted, gold, Green Published, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000396575500094,
Author = {Hu, Yanhui and Comjean, Aram and Roesel, Charles and Vinayagam,
   Arunachalam and Flockhart, Ian and Zirin, Jonathan and Perkins, Lizabeth
   and Perrimon, Norbert and Mohr, Stephanie E.},
Title = {FlyRNAi.org-the database of the <i>Drosophila</i> RNAi screening center
   and transgenic RNAi project: 2017 update},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2017},
Volume = {45},
Number = {D1},
Pages = {D672-D678},
Month = {JAN 4},
Abstract = {The FlyRNAi database of the Drosophila RNAi Screening Center (DRSC) and
   Transgenic RNAi Project (TRiP) at Harvard Medical School and associated
   DRSC/TRiP Functional Genomics Resources website
   (http://fgr.hms.harvard.edu) serve as a reagent production tracking
   system, screen data repository, and portal to the community. Through
   this portal, we make available protocols, online tools, and other
   resources useful to researchers at all stages of high-throughput
   functional genomics screening, from assay design and reagent
   identification to data analysis and interpretation. In this update, we
   describe recent changes and additions to our website, database and suite
   of online tools. Recent changes reflect a shift in our focus from a
   single technology (RNAi) and model species (Drosophila) to the
   application of additional technologies (e.g. CRISPR) and support of
   integrated, cross-species approaches to uncovering gene function using
   functional genomics and other approaches.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Mohr, SE (Corresponding Author), Harvard Med Sch, Dept Genet, 77 Ave Louis Pasteur, Boston, MA 02115 USA.
   Mohr, SE (Corresponding Author), Harvard Med Sch, Drosophila RNAi Screening Ctr, 77 Ave Louis Pasteur, Boston, MA 02115 USA.
   Mohr, SE (Corresponding Author), Harvard Med Sch, Transgen RNAi Project, 77 Ave Louis Pasteur, Boston, MA 02115 USA.
   Hu, Yanhui; Comjean, Aram; Roesel, Charles; Vinayagam, Arunachalam; Flockhart, Ian; Zirin, Jonathan; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E., Harvard Med Sch, Dept Genet, 77 Ave Louis Pasteur, Boston, MA 02115 USA.
   Hu, Yanhui; Comjean, Aram; Roesel, Charles; Vinayagam, Arunachalam; Flockhart, Ian; Zirin, Jonathan; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E., Harvard Med Sch, Drosophila RNAi Screening Ctr, 77 Ave Louis Pasteur, Boston, MA 02115 USA.
   Hu, Yanhui; Comjean, Aram; Roesel, Charles; Vinayagam, Arunachalam; Flockhart, Ian; Zirin, Jonathan; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E., Harvard Med Sch, Transgen RNAi Project, 77 Ave Louis Pasteur, Boston, MA 02115 USA.
   Roesel, Charles, Northeastern Univ, Marine Sci Ctr, 430 Nahant Rd, Nahant, MA 01908 USA.
   Perrimon, Norbert, Howard Hughes Med Inst, 77 Ave Louis Pasteur, Boston, MA 02115 USA.},
DOI = {10.1093/nar/gkw977},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {CULTURED-CELLS; RESOURCES; PREDICTION; ORTHOLOGS; GUIDE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {stephanie\_mohr@hms.harvard.edu},
Affiliations = {Harvard University; Harvard Medical School; Harvard University; Harvard
   Medical School; Harvard University; Harvard Medical School; Northeastern
   University; Howard Hughes Medical Institute},
ResearcherID-Numbers = {Roesel, Charles L/U-3697-2018
   Perrimon, Norbert/F-9766-2011
   },
ORCID-Numbers = {Roesel, Charles L/0000-0001-5608-1979
   Mohr, Stephanie/0000-0001-9639-7708},
Funding-Acknowledgement = {NIH NIGMS {[}R01 GM067761, NIGMS R01 GM084947]; NIH {[}R24 RR032668, R24
   OD021997]; Dana Farber/Harvard Cancer Center {[}NCI Cancer Center]
   {[}NIH 5 P30 CA06516]; NIH; Howard Hughes Medical Institute},
Funding-Text = {NIH NIGMS {[}R01 GM067761, NIGMS R01 GM084947]; NIH {[}R24 RR032668, R24
   OD021997 to N.P., P.I.]; Dana Farber/Harvard Cancer Center {[}NCI Cancer
   Center Support Grant \# NIH 5 P30 CA06516 to S.E.M.]; Howard Hughes
   Medical Institute (to N.P.). Funding for open access charge: NIH.},
Number-of-Cited-References = {28},
Times-Cited = {33},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {EO3DQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000396575500094},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000462587400083,
Author = {Lombardot, Thierry and Morgat, Anne and Axelsen, Kristian B. and Aimo,
   Lucila and Hyka-Nouspikel, Nevila and Niknejad, Anne and Ignatchenko,
   Alex and Xenarios, Ioannis and Coudert, Elisabeth and Redaschi, Nicole
   and Bridge, Alan},
Title = {Updates in Rhea: SPARQLing biochemical reaction data},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2019},
Volume = {47},
Number = {D1},
Pages = {D596-D600},
Month = {JAN 8},
Abstract = {Rhea (http://www.rhea-db.org) is a comprehensive and non-redundant
   resource of over 11 000 expert-curated biochemical reactions that uses
   chemical entities from the ChEBI ontology to represent reaction
   participants. Originally designed as an annotation vocabulary for the
   UniProt Knowledgebase (UniProtKB), Rhea also provides reaction data for
   a range of other core knowledgebases and data repositories including
   ChEBI and MetaboLights. Here we describe recent developments in Rhea,
   focusing on a new resource description framework representation of Rhea
   reaction data and an SPARQL endpoint (https://sparql.rhea-db.org/sparql)
   that provides access to it. We demonstrate how federated queries that
   combine the Rhea SPARQL endpoint and other SPARQL endpoints such as that
   of UniProt can provide improved metabolite annotation and support
   integrative analyses that link the metabolome through the proteome to
   the transcriptome and genome. These developments will significantly
   boost the utility of Rhea as a means to link chemistry and biology for a
   more holistic understanding of biological systems and their function in
   health and disease.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bridge, A (Corresponding Author), SIB Swiss Inst Bioinformat, CMU, Swiss Prot Grp, 1 Rue Michel Servet, CH-1211 Geneva 4, Switzerland.
   Lombardot, Thierry; Morgat, Anne; Axelsen, Kristian B.; Aimo, Lucila; Hyka-Nouspikel, Nevila; Coudert, Elisabeth; Redaschi, Nicole; Bridge, Alan, SIB Swiss Inst Bioinformat, CMU, Swiss Prot Grp, 1 Rue Michel Servet, CH-1211 Geneva 4, Switzerland.
   Niknejad, Anne, SIB Swiss Inst Bioinformat, Vital IT Grp, Batiment Genopode, CH-1015 Lausanne, Switzerland.
   Ignatchenko, Alex, EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Xenarios, Ioannis, Univ Geneva, Dept Biochem, CH-1211 Geneva, Switzerland.
   Xenarios, Ioannis, Univ Lausanne, Ctr Integrat Genom, CH-1015 Lausanne, Switzerland.},
DOI = {10.1093/nar/gky876},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {ENZYME; METABOLITES; PATHWAYS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {alan.bridge@sib.swiss},
Affiliations = {Swiss Institute of Bioinformatics; Swiss Institute of Bioinformatics;
   European Molecular Biology Laboratory (EMBL); Wellcome Trust Sanger
   Institute; University of Geneva; University of Lausanne},
ResearcherID-Numbers = {Axelsen, Kristian B/F-3449-2015
   Xenarios, Ioannis/ABD-5045-2021
   Bridge, Alan/U-4209-2018},
ORCID-Numbers = {Axelsen, Kristian B/0000-0003-3889-2879
   Xenarios, Ioannis/0000-0002-3413-6841
   Ignatchenko, Alexandr/0000-0002-6083-941X
   Hyka-Nouspikel, Nevila/0000-0001-7855-209X
   Morgat, Anne/0000-0002-1216-2969
   Lombardot, Thierry/0000-0003-4157-0029
   Redaschi, Nicole/0000-0001-8890-2268
   Bridge, Alan/0000-0003-2148-9135},
Funding-Acknowledgement = {Swiss Federal Government through the State Secretariat for Education,
   Research and Innovation (SERI); SwissLipids project of the SystemsX.ch,
   the Swiss Initiative in Systems Biology; EMBL; ELIXIR Implementation
   study on `A microbial metabolism resource for Systems Biology'; SERI},
Funding-Text = {Swiss Federal Government through the State Secretariat for Education,
   Research and Innovation (SERI); SwissLipids project of the SystemsX.ch,
   the Swiss Initiative in Systems Biology (in part); EMBL; ELIXIR
   Implementation study on `A microbial metabolism resource for Systems
   Biology' (in part). Funding for open access charge: SERI.},
Number-of-Cited-References = {27},
Times-Cited = {39},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {HQ7GH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000462587400083},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000525956700136,
Author = {Togninalli, Matteo and Seren, Uemit and Freudenthal, Jan A. and Monroe,
   J. Grey and Meng, Dazhe and Nordborg, Magnus and Weigel, Detlef and
   Borgwardt, Karsten and Korte, Arthur and Grimm, Dominik G.},
Title = {AraPheno and the AraGWAS Catalog 2020: a major database update including
   RNA-Seq and knockout mutation data for <i>Arabidopsis thaliana</i>},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2020},
Volume = {48},
Number = {D1},
Pages = {D1063-D1068},
Month = {JAN 8},
Abstract = {Genome-wide association studies (GWAS) are integral for studying
   genotype-phenotype relationships and gaining a deeper understanding of
   the genetic architecture underlying trait variation. A plethora of
   genetic associations between distinct loci and various traits have been
   successfully discovered and published for the model plant Arabidopsis
   thaliana. This success and the free availability of full genomes and
   phenotypic data for more than 1,000 different natural inbred lines led
   to the development of several data repositories. AraPheno
   (https://arapheno.1001genomes.org ) serves as a central repository of
   population-scale phenotypes in A. thaliana, while the AraGWAS Catalog
   (https://aragwas.1001genomes. org ) provides a publicly available,
   manually curated and standardized collection of marker-trait
   associations for all available phenotypes from AraPheno. In this major
   update, we introduce the next generation of both platforms, including
   new data, features and tools. We included novel results on associations
   between knockout-mutations and all AraPheno traits. Furthermore,
   AraPheno has been extended to display RNA-Seq data for hundreds of
   accessions, providing expression information for over 28 000 genes for
   these accessions. All data, including the imputed genotype matrix used
   for GWAS, are easily downloadable via the respective databases.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Korte, A (Corresponding Author), Univ Wurzburg, Ctr Computat \& Theoret Biol, Wurzburg, Germany.
   Grimm, DG (Corresponding Author), Tech Univ Munich, TUM Campus Straubing Biotechnol \& Sustainabil Bio, Straubing, Germany.
   Grimm, DG (Corresponding Author), Weihenstephan Triesdorf Univ Appl Sci, Bioinformat, Straubing, Germany.
   Togninalli, Matteo; Borgwardt, Karsten, Swiss Fed Inst Technol, Machine Learning \& Computat Biol Lab, Dept Biosyst Sci \& Engn, Basel, Switzerland.
   Togninalli, Matteo; Borgwardt, Karsten, Swiss Inst Bioinformat, Basel, Switzerland.
   Seren, Uemit; Meng, Dazhe; Nordborg, Magnus, Gregor Mendel Inst Mol Plant Biol, Vienna, Austria.
   Freudenthal, Jan A.; Korte, Arthur, Univ Wurzburg, Ctr Computat \& Theoret Biol, Wurzburg, Germany.
   Monroe, J. Grey; Weigel, Detlef, Max Planck Inst Dev Biol, Tubingen, Germany.
   Meng, Dazhe, Google, Mountain View, CA USA.
   Grimm, Dominik G., Tech Univ Munich, TUM Campus Straubing Biotechnol \& Sustainabil Bio, Straubing, Germany.
   Grimm, Dominik G., Weihenstephan Triesdorf Univ Appl Sci, Bioinformat, Straubing, Germany.},
DOI = {10.1093/nar/gkz925},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {NATURAL VARIATION; OPPORTUNITIES},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {arthur.korte@uni-wuerzburg.de
   dominik.grimm@hswt.de},
Affiliations = {Swiss Federal Institutes of Technology Domain; ETH Zurich; Swiss
   Institute of Bioinformatics; Austrian Academy of Sciences; Vienna
   Biocenter (VBC); Gregor Mendel Institute of Molecular Plant Biology
   (GMI); University of Wurzburg; Max Planck Society; Google Incorporated;
   Technical University of Munich},
ResearcherID-Numbers = {Weigel, Detlef/GSJ-0799-2022
   Weigel, Detlef/C-1418-2008
   Grimm, Dominik/L-9088-2019
   Weigel, Detlef/AAR-3312-2021
   Korte, Arthur/H-3190-2019
   },
ORCID-Numbers = {Weigel, Detlef/0000-0002-2114-7963
   Weigel, Detlef/0000-0002-2114-7963
   Grimm, Dominik/0000-0003-2085-4591
   Korte, Arthur/0000-0003-0831-1463
   Monroe, Grey/0000-0002-4025-5572
   Borgwardt, Karsten/0000-0001-7221-2393
   Nordborg, Magnus/0000-0001-7178-9748},
Funding-Acknowledgement = {NSF {[}1701918]; German Research Foundation (DFG); Technical University
   of Munich (TUM); Division Of Environmental Biology; Direct For
   Biological Sciences {[}1701918] Funding Source: National Science
   Foundation},
Funding-Text = {NSF Award {[}1701918 to J.G.M.]. This work was supported by the German
   Research Foundation (DFG) and the Technical University of Munich (TUM)
   in the framework of the Open Access Publishing Program.},
Number-of-Cited-References = {41},
Times-Cited = {36},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {LD3UB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000525956700136},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000644834400004,
Author = {Chousianitis, Konstantinos and Papanikolaou, Xanthos and Drakatos,
   George and Tselentis, G-Akis},
Title = {NOANET: A Continuously Operating GNSS Network for Solid-Earth Sciences
   in Greece},
Journal = {SEISMOLOGICAL RESEARCH LETTERS},
Year = {2021},
Volume = {92},
Number = {3},
Pages = {2050-2064},
Month = {MAY},
Abstract = {The NOANET network is a continuously operating high-rate Global
   Navigation Satellite System (GNSS) network in Greece whose primary role
   is to enhance and support geo-physical research employing GNSS data.
   This network is operated by the Institute of Geodynamics of the National
   Observatory of Athens and currently (September 2020) consists of 26
   stations, most of which are located close to major seismogenic
   structures of Greece to optimally measure tectonic and seismically
   induced motions. All NOANET receivers are configured to record and
   collect data with a sampling rate of 1 Hz, although some of them also
   collect data every 5 Hz on their ring buffer. The network is committed
   to free and open data sharing within the scientific community, and the
   collected data are made available via the NOANET data repository and
   distribution point for all interested parties with no limitations.
   Integrity, validity, and quality checks of the acquired data are
   performed using a variety of software tools along with in-house
   developed programs to supervise the network performance and detect
   ill-formed data and/or awkward station behavior. In addition, the
   conventional low-rate GNSS observation data of all NOANET stations are
   routinely processed on a daily basis to supervise their performance
   through their position time series. Since the beginning of its
   establishment, the NOANET network has recorded a variety of deformation
   sig-nals, and a large number of published papers have used GNSS data
   from stations that are part of NOANET to constrain, model, and interpret
   the nature of the associated geo-physical phenomena.},
Publisher = {SEISMOLOGICAL SOC AMER},
Address = {400 EVELYN AVE, SUITE 201, ALBANY, CA 94706-1375 USA},
Type = {Article},
Language = {English},
Affiliation = {Chousianitis, K (Corresponding Author), Natl Observ Athens, Inst Geodynam, Athens, Greece.
   Chousianitis, Konstantinos; Papanikolaou, Xanthos; Drakatos, George; Tselentis, G-Akis, Natl Observ Athens, Inst Geodynam, Athens, Greece.},
DOI = {10.1785/0220200340},
ISSN = {0895-0695},
EISSN = {1938-2057},
Keywords-Plus = {GEODETIC EVIDENCE; ACTIVE TECTONICS; COSEISMIC SLIP; IONIAN SEA; GPS;
   DEFORMATION; FAULT; STRAIN; NORTH; EARTHQUAKES},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {chousianitis@noa.gr},
Affiliations = {National Observatory of Athens},
ResearcherID-Numbers = {Chousianitis, Konstantinos/P-6237-2016
   Drakatos, George/ABD-3308-2021
   },
ORCID-Numbers = {Chousianitis, Konstantinos/0000-0001-7755-5205
   Drakatos, George/0000-0002-4647-3984
   Papanikolaou, Xanthos/0000-0002-2427-5960},
Funding-Acknowledgement = {General Secretariat for Research and Technology of Greece (GSRT);
   Directorate-General for European Civil Protection and Humanitarian Aid
   Operations; European Regional Development Fund of the European Union;
   European Economic Area (EEA) Funding Mechanism},
Funding-Text = {The authors are grateful to Athanassios Ganas for his fundamental
   contribution and support in the development and management of the NOANET
   network since 2006. The authors are indebted to Panagiotis Grigorakakis
   of METRICA S.A. for his technical expertise, advice, and software
   support. The authors thank everyone from the staff of the National
   Observatory of Athens (NOA) who has helped with the installation of the
   instruments, the IT administration, and the technical support of NOANET
   with special acknowledgement to Marios Papanikolaou, Kostas Boukouras,
   Panagiotis Argyrakis, Theodore Chinis, Kyriakos Kontakos, Stratos
   Liadopoulos, and Michalis Samios. The NOANET Global Navigation Satellite
   System (GNSS) network has received funding from a variety of sources,
   including the General Secretariat for Research and Technology of Greece
   (GSRT), the Directorate-General for European Civil Protection and
   Humanitarian Aid Operations, and the European Regional Development Fund
   of the European Union and the European Economic Area (EEA) Funding
   Mechanism. The authors benefitted from discussions with Antonio Avallone
   and Giulio Selvaggi, and the authors thank them for reviewing the draft
   version of this article. The Associate Editor Taka'aki Taira and one
   anonymous reviewer are gratefully acknowledged for constructive comments
   that greatly improved this article.},
Number-of-Cited-References = {56},
Times-Cited = {13},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Seismol. Res. Lett.},
Doc-Delivery-Number = {RU0HZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000644834400004},
DA = {2024-01-15},
}

@article{ WOS:000562474100080,
Author = {Ge, Xiaoyu and Raghu, Vineet K. and Chrysanthis, Panos K. and Benos, V,
   Panayiotis},
Title = {CausalMGM: an interactive web-based causal discovery tool},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2020},
Volume = {48},
Number = {W1},
Pages = {W597-W602},
Month = {JUL 2},
Abstract = {High-throughput sequencing and the availability of large online data
   repositories (e.g. The Cancer Genome Atlas and Trans-Omics for Precision
   Medicine) have the potential to revolutionize systems biology by
   enabling researchers to study interactions between data from different
   modalities (i.e. genetic, genomic, clinical, behavioral, etc.).
   Currently, data mining and statistical approaches are confined to
   identifying correlates in these datasets, but researchers are often
   interested in identifying cause-and-effect relationships. Causal
   discovery methods were developed to infer such cause-and-effect
   relationships from observational data. Though these algorithms have had
   demonstrated successes in several biomedical applications, they are
   difficult to use for non-experts. So, there is a need for web-based
   tools to make causal discovery methods accessible. Here, we present
   CausalMGM (http://causalmgm.org/), the first web-based causal discovery
   tool that enables researchers to find cause-and-effect relationships
   from observational data. Web-based CausalMGM consists of three data
   analysis tools: (i) feature selection and clustering; (ii) automated
   identification of cause-and-effect relationships via a graphical model;
   and (iii) interactive visualization of the learned causal (directed)
   graph. We demonstrate how CausalMGM enables an end-to-end exploratory
   analysis of biomedical datasets, giving researchers a clearer picture of
   its capabilities.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Chrysanthis, PK; Benos, PV (Corresponding Author), Univ Pittsburgh, Dept Comp Sci, 4200 Fifth Ave, Pittsburgh, PA 15260 USA.
   Benos, PV (Corresponding Author), Univ Pittsburgh, Dept Computat \& Syst Biol, 3420 Forbes Ave, Pittsburgh, PA 15213 USA.
   Ge, Xiaoyu; Raghu, Vineet K.; Chrysanthis, Panos K.; Benos, Panayiotis, V, Univ Pittsburgh, Dept Comp Sci, 4200 Fifth Ave, Pittsburgh, PA 15260 USA.
   Raghu, Vineet K.; Benos, Panayiotis, V, Univ Pittsburgh, Dept Computat \& Syst Biol, 3420 Forbes Ave, Pittsburgh, PA 15213 USA.},
DOI = {10.1093/nar/gkaa350},
ISSN = {0305-1048},
EISSN = {1362-4962},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {panos@cs.pitt.edu
   benos@pitt.edu},
Affiliations = {Pennsylvania Commonwealth System of Higher Education (PCSHE); University
   of Pittsburgh; Pennsylvania Commonwealth System of Higher Education
   (PCSHE); University of Pittsburgh},
ORCID-Numbers = {Benos, Panayiotis/0000-0003-3172-3132
   Chrysanthis, Panos/0000-0001-7189-9816},
Funding-Acknowledgement = {National Institutes of Health {[}U01HL137159, R01L M012087, T32CA082084,
   R01LM012087]},
Funding-Text = {National Institutes of Health {[}U01HL137159 and R01L M012087 to P.V.B.;
   T32CA082084 to V.K.R.]. Funding for open access charge: National
   Institutes of Health {[}R01LM012087].},
Number-of-Cited-References = {24},
Times-Cited = {6},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {NE3CJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000562474100080},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000743496700141,
Author = {Martini, Cari and Liu, Ying Frances and Gong, Hui and Sayers, Nicole and
   Segura, German and Fostel, Jennifer},
Title = {CEBS update: curated toxicology database with enhanced tools for data
   integration},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2022},
Volume = {50},
Number = {D1},
Pages = {D1156-D1163},
Month = {JAN 7},
Abstract = {The Chemical Effects in Biological Systems database (CEBS) contains
   extensive toxicology study results and metadata from the Division of the
   National Toxicology Program (NTP) and other studies of environmental
   health interest. This resource grants public access to search and
   collate data from over 10 250 studies for 12 750 test articles
   (chemicals, environmental agents). CEBS has made considerable strides
   over the last 5 years to integrate growing internal data repositories
   into data warehouses and data marts to better serve the public with high
   quality curated datasets. This effort includes harmonizing legacy terms
   and metadata to current standards, mapping test articles to external
   identifiers, and aligning terms to OBO (Open Biological and Biomedical
   Ontology) Foundry ontologies. The data are made available through the
   CEBS Homepage (https://cebs.niehs.nih.gov/cebs/), guided search
   applications, flat files on FTP (file transfer protocol), and APIs
   (application programming interface) for user access and to provide a
   bridge for computational tools. The user interface is intuitive with a
   single search bar to query keywords related to study metadata,
   publications, and data availability. Results are consolidated to single
   pages for each test article with NTP conclusions, publications,
   individual studies, data collections, and links to related test articles
   and projects available together.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Fostel, J (Corresponding Author), Natl Inst Environm Hlth Sci, Div Natl Toxicol Program, POB 12233, Res Triangle Pk, NC 27709 USA.
   Martini, Cari; Liu, Ying Frances; Gong, Hui; Sayers, Nicole; Segura, German, ASRC Fed, 430 Davis Dr,Suite 400, Morrisville, NC 27560 USA.
   Fostel, Jennifer, Natl Inst Environm Hlth Sci, Div Natl Toxicol Program, POB 12233, Res Triangle Pk, NC 27709 USA.},
DOI = {10.1093/nar/gkab981},
EarlyAccessDate = {NOV 2021},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {TOXICOGENOMICS SIGNATURE; CHEMICALS; TOXICITY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {fostel@nih.gov},
Affiliations = {National Institutes of Health (NIH) - USA; NIH National Institute of
   Environmental Health Sciences (NIEHS)},
Funding-Acknowledgement = {ASRC Federal under National Institute of Environmental Health Sciences
   {[}HHSN31620120054W, HHSN273201000063U GS06F0629Z]; NIEHS},
Funding-Text = {ASRC Federal under National Institute of Environmental Health Sciences
   contracts `Support for Toxicological Data for the National Toxicology
   Program' {[}HHSN31620120054W and HHSN273201000063U GS06F0629Z]. Funding
   for open access charge: NIEHS.},
Number-of-Cited-References = {32},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {YH9RO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000743496700141},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000587949900003,
Author = {Al-Khuzaie, Marwah M. and Janna, Hussein and Al-Ansari, Nadhir},
Title = {Assessment model of water harvesting and storage location using GIS and
   remote sensing in Al-Qadisiyah, Iraq},
Journal = {ARABIAN JOURNAL OF GEOSCIENCES},
Year = {2020},
Volume = {13},
Number = {21},
Month = {OCT 28},
Abstract = {One of the important steps towards optimizing land productivity and
   water availability for the semi-arid and arid areas is the
   identification of potential sites for water harvesting. Therefore, this
   paper uses the Geographical Information System (GIS) techniques to
   select the optimized sites for water harvesting in Al-Qadisiyah
   Governorate, Iraq. Geographic water management capabilities are applied
   as a spatial analysis model. Data from global data repositories are
   retrieved followed by rescaling them to a spatial resolution to acquire
   a manageable input data set. The Soil Conservation Service Curve Number
   (SCS-CN) model is used to calculate the potential runoff as an
   intermediate input. Multi-Criteria Evaluation techniques are adopted to
   identify the relative importance and suitability levels of the input
   parameters set to manage the water supply. The suitability for
   identifying irrigation pond and dam location(s) was considered in this
   study. To achieve this goal, the criteria for eligibility for water
   harvesting areas have been completed on the basis of the conditions in
   the study methods. Based on the hydrological and geomorphological
   standards of the study area, suitable sites for harvest areas were
   identified and it was divided into four classes in terms of their
   suitability for water harvesting, namely very low, low, moderate, and
   high suitable for water harvesting. It can be concluded that the
   findings of this research can be used to assist in water resources
   management as an efficient planning tool to ensure sustainable
   development of the water in Iraq who suffers from water shortages.},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Al-Khuzaie, MM (Corresponding Author), Univ Al Qadisiyah, Coll Engn, Civil Engn Dept, Al Qadisiyah, Iraq.
   Al-Khuzaie, Marwah M.; Janna, Hussein, Univ Al Qadisiyah, Coll Engn, Civil Engn Dept, Al Qadisiyah, Iraq.
   Al-Ansari, Nadhir, Lulea Univ, Dept Civil Environmenta \& Nat Resources Engn, Lulea, Sweden.},
DOI = {10.1007/s12517-020-06154-4},
Article-Number = {1154},
ISSN = {1866-7511},
EISSN = {1866-7538},
Keywords = {Water availability; Remote sensing; Clean water quality; Rainwater
   harvesting; Runoff; Multi-criteria; GIS},
Keywords-Plus = {DECISION-MAKING; POTENTIAL SITES; RAINWATER; SOIL},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {marwah.alkhuzaie@qu.edu.iq
   hussein.janna@qu.edu.iq
   nadhir.alansari@ltu.se},
Affiliations = {University of Al-Qadisiyah; Lulea University of Technology},
ResearcherID-Numbers = {Janna, Hussein/M-4278-2017
   },
ORCID-Numbers = {Janna, Hussein/0000-0002-7635-7992
   M. Al-Khuzaie, Marwah/0000-0002-7834-9566
   Al-Ansari, Nadhir/0000-0002-6790-2653},
Funding-Acknowledgement = {Lulea University of Technology},
Funding-Text = {Open access funding provided by Lulea University of Technology.},
Number-of-Cited-References = {29},
Times-Cited = {11},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {20},
Journal-ISO = {Arab. J. Geosci.},
Doc-Delivery-Number = {OP2YN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000587949900003},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000207785300006,
Author = {King, Todd and Narock, Tom and Walker, Raymond and Merka, Jan and Joy,
   Steven},
Title = {A brave new (virtual) world: distributed searches, relevance scoring and
   facets},
Journal = {EARTH SCIENCE INFORMATICS},
Year = {2008},
Volume = {1},
Number = {1},
Pages = {29-34},
Month = {APR},
Abstract = {Our ability to deal with complex systems has improved through
   information system research which includes improved modeling (both data
   and system), the use of semantics and advances in distributed computing.
   The past decade has seen an explosion in the amount and variety of
   geosciences data and the emergence of true open data repositories
   through which scientists can freely access this data. Those data are
   found in thousands of repositories located around the world. Virtual
   observatories have been created to address the challenge of helping
   scientists search those repositories to find and access the required
   data. This challenge is been addressed by using technologies such as the
   Internet (with ample connectivity and bandwidth), the Web, cheap
   computing power, cheap storage and standards for critical components.
   Many scientific disciplines are developing virtual observatories. Yet
   some of the most compelling science questions cross multiple domains.
   While semantics can provide cross domain reasoning, often the first step
   in answering a question is determining what resources are available
   which may be relevant to a topic. The topic can be expressed as simple
   phrases or word sequences. Using a common relevance scoring method at
   all locations can enable a federated search across loosely coupled
   providers. The results of which can be organized into facets to aid the
   user in selecting the most promising resources with which to pursue the
   scientific investigation. We describe an approach to developing and
   deploying relevance scoring methods and faceted results in this brave
   new (virtual) world. We have found that a scoring method which considers
   both the presence of terms and the proximity of these terms relative to
   the order of the terms in the query improves the assessment of
   relevance. We call this Term Presence-Proximity (TPP) scoring and
   describe a method for calculating a normalized score. TPP scoring
   compares favorably with other scoring approaches.},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {King, T (Corresponding Author), Univ Calif Los Angeles, Inst Geophys \& Planetary Phys, Los Angeles, CA 90024 USA.
   King, Todd; Walker, Raymond; Joy, Steven, Univ Calif Los Angeles, Inst Geophys \& Planetary Phys, Los Angeles, CA 90024 USA.
   Narock, Tom; Merka, Jan, Univ Maryland Baltimore Cty, Goddard Earth Sci \& Technol Ctr, Baltimore, MD 21228 USA.
   Narock, Tom; Merka, Jan, NASA, Goddard Space Flight Ctr, Heliospher Phys Lab, Greenbelt, MD 20771 USA.},
DOI = {10.1007/s12145-008-0002-7},
ISSN = {1865-0473},
Keywords = {Relevance scoring facets virtual observatory search},
Research-Areas = {Computer Science; Geology},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Geosciences,
   Multidisciplinary},
Author-Email = {tking@igpp.ucla.edu},
Affiliations = {University of California System; University of California Los Angeles;
   National Aeronautics \& Space Administration (NASA); NASA Goddard Space
   Flight Center; University System of Maryland; University of Maryland
   Baltimore County; National Aeronautics \& Space Administration (NASA);
   NASA Goddard Space Flight Center},
ORCID-Numbers = {Narock, Tom/0000-0002-9785-4496},
Funding-Acknowledgement = {National Aeronautics and Space Administration {[}NNX07AC95G,
   NNX07AC93G]; Virtual Observatories for Solar and Space Physics Data
   {[}S3CVO]},
Funding-Text = {This work was supported by the National Aeronautics and Space
   Administration under Grants No. NNX07AC95G and NNX07AC93G and issued
   through the Virtual Observatories for Solar and Space Physics Data
   (S3CVO). The UCLA/IGPP publication number is 6360.},
Number-of-Cited-References = {10},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Earth Sci. Inform.},
Doc-Delivery-Number = {V15EM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000207785300006},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000455007300004,
Author = {Tenopir, C. and Christian, L. and Allard, S. and Borycz, J.},
Title = {Research Data Sharing: Practices and Attitudes of Geophysicists},
Journal = {EARTH AND SPACE SCIENCE},
Year = {2018},
Volume = {5},
Number = {12},
Pages = {891-902},
Month = {DEC},
Abstract = {Open data policies have been introduced by governments, funders, and
   publishers over the past decade. Previous research showed a growing
   recognition by scientists of the benefits of data-sharing and reuse, but
   actual practices lag and are not always compliant with new regulations.
   The goal of this study is to investigate motives, attitudes, and data
   practices of the community of Earth and planetary geophysicists, a
   discipline believed to have accepting attitudes toward data sharing and
   reuse. A better understanding of the attitudes and current data-sharing
   practices of this scientific community could enable funders, publishers,
   data managers, and librarians to design systems and services that help
   scientists understand and adhere to mandates and to create practices,
   tools, and services that are scientist-focused. An online survey was
   distributed to the members of the American Geophysical Union, producing
   1,372 responses from 116 countries. The attitudes of researchers to data
   sharing and reuse were generally positive, but in practice, scientists
   had concerns about sharing their own research data. These concerns
   include the possibility of potential data misuse and the need for
   assurance of proper citation and acknowledgement. Training and
   assistance in good data management practices are lacking in many
   scientific fields and might help to alleviate these doubts.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Tenopir, C (Corresponding Author), Univ Tennessee, Sch Informat Sci, Knoxville, TN 37996 USA.
   Tenopir, C.; Christian, L.; Allard, S.; Borycz, J., Univ Tennessee, Sch Informat Sci, Knoxville, TN 37996 USA.},
DOI = {10.1029/2018EA000461},
ISSN = {2333-5084},
Keywords-Plus = {OPEN DATA POLICIES},
Research-Areas = {Astronomy \& Astrophysics; Geology},
Web-of-Science-Categories  = {Astronomy \& Astrophysics; Geosciences, Multidisciplinary},
Author-Email = {ctenopir@utk.edu},
Affiliations = {University of Tennessee System; University of Tennessee Knoxville},
ResearcherID-Numbers = {Borycz, Joshua Daniel/ACF-2328-2022
   Borycz, Joshua/N-2010-2019
   },
ORCID-Numbers = {Borycz, Joshua/0000-0002-1505-148X
   Tenopir, Carol/0000-0002-9056-8251
   Allard, Suzie/0000-0001-9421-3848},
Funding-Acknowledgement = {National Science Foundation (NSF) {[}080944]},
Funding-Text = {This project, Data Observation Network for Earth (DataONE), is funded by
   the National Science Foundation (NSF), award 080944, under a cooperative
   agreement, William Michener, Principal Investigator. NSF had no role in
   the research design, data collection, data analysis, nor in the writing
   of this paper or the decision where to publish. The authors of this
   article have no conflicts of interest to declare. We would like to thank
   the American Geophysical Union for their assistance, in particular
   Brooks Hanson, AGU Executive Vice President of Science. We would also
   like to thank Natalie Rice of the Center for Information and
   Communication Studies (University of Tennessee), and graduate research
   assistants Paris Whalon and Hannah Blanco, also of the University of
   Tennessee. The data for this study can be found in the Dryad data
   repository at the time of publication.},
Number-of-Cited-References = {32},
Times-Cited = {29},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {33},
Journal-ISO = {Earth Space Sci.},
Doc-Delivery-Number = {HG5HN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000455007300004},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000940322000001,
Author = {Palacios, Daniel M. and Cantor, Mauricio},
Title = {Priorities for ecological research on cetaceans in the Galapagos Islands},
Journal = {FRONTIERS IN MARINE SCIENCE},
Year = {2023},
Volume = {10},
Month = {FEB 14},
Abstract = {Located in the eastern tropical Pacific, the Galapagos Islands are an
   oceanic insular ecosystem subject to strong environmental variability
   driven by local and regional processes. Past research has shown that
   such conditions can attract and sustain at least 23 cetacean species,
   out of which 14 are common, including nine Delphinids, one Ziphiid, one
   Physeterid, and three Balaenopterids. These species occupy both coastal
   and oceanic habitats, most are present year-round, and a few are
   migratory. However, research on cetaceans in Galapagos has been sporadic
   and chronically underfunded and is not currently considered a priority
   in the research agenda for Galapagos. Based on a review of existing
   information and an assessment of knowledge gaps, here we identify
   priorities for ecological research on cetaceans in Galapagos along five
   topical areas: 1) spatiotemporal occurrence, 2) population assessment,
   3) health assessment, 4) social ecology, and 5) trophic ecology.
   Addressing these knowledge gaps will also help inform actions to
   preserve cetacean biodiversity and to manage human activities involving
   or affecting cetaceans in Galapagos. Given the logistical and funding
   challenges of conducting cetacean research in Galapagos, we recommend
   optimizing data sampling and accessibility via integrated research
   protocols and open data repositories. We also recommend capitalizing on
   local citizen science activities, such as those conducted from cruise
   ships and whale-watching tours, which can serve as platforms of
   opportunity for obtaining basic data, thereby contributing to long-term
   data acquisition. Our proposed priorities should be assessed by
   Ecuadorian and Galapagos governmental institutions in broad and
   inclusive consultation with stakeholders and the scientific community
   prior to development and implementation of a research agenda.
   Collectively, these efforts will advance our understanding of the
   ecological role that marine megafauna, such as cetaceans, play in
   Galapagos and other oceanic islands, including maintaining large-scale
   connectivity and mitigating climate change.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Palacios, DM (Corresponding Author), Oregon State Univ, Marine Mammal Inst, Newport, OR 97365 USA.
   Palacios, DM (Corresponding Author), Oregon State Univ, Dept Fisheries Wildlife \& Conservat Sci, Newport, OR 97365 USA.
   Palacios, Daniel M.; Cantor, Mauricio, Oregon State Univ, Marine Mammal Inst, Newport, OR 97365 USA.
   Palacios, Daniel M.; Cantor, Mauricio, Oregon State Univ, Dept Fisheries Wildlife \& Conservat Sci, Newport, OR 97365 USA.},
DOI = {10.3389/fmars.2023.1084057},
Article-Number = {1084057},
EISSN = {2296-7745},
Keywords = {cetaceans; megafauna; Galapagos Islands; eastern tropical Pacific;
   oceanic insular ecosystems; migratory connectivity; research priorities;
   questions; participatory research agenda},
Keywords-Plus = {WHALES PHYSETER-MACROCEPHALUS; BOTTLE-NOSED DOLPHINS; SEA-SURFACE
   TEMPERATURE; ROUGH-TOOTHED DOLPHINS; SPERM-WHALES; HABITAT USE; MARINE
   RESERVE; TURSIOPS-TRUNCATUS; MOVEMENT PATTERNS; SEASONAL PATTERNS},
Research-Areas = {Environmental Sciences \& Ecology; Marine \& Freshwater Biology},
Web-of-Science-Categories  = {Environmental Sciences; Marine \& Freshwater Biology},
Author-Email = {daniel.palacios@oregonstate.edu},
Affiliations = {Oregon State University; Oregon State University},
ResearcherID-Numbers = {Cantor, Mauricio/GQP-2849-2022},
ORCID-Numbers = {Cantor, Mauricio/0000-0002-0019-5106},
Funding-Acknowledgement = {Endowed Professorship in Whale Habitats at Oregon State University;
   Marine Mammal Research Program Fund; Jungers Faculty Development and
   Research Fund; Marine Studies Initiative; College of Agricultural
   Sciences},
Funding-Text = {DP was supported by the Endowed Professorship in Whale Habitats at
   Oregon State University. MC was supported by the Marine Mammal Research
   Program Fund and the Jungers Faculty Development and Research Fund, the
   Marine Studies Initiative, and the College of Agricultural Sciences, all
   at Oregon State University.},
Number-of-Cited-References = {246},
Times-Cited = {0},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Front. Mar. Sci.},
Doc-Delivery-Number = {9J6VP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000940322000001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000462551600002,
Author = {Peters, Kristian and Bradbury, James and Bergmann, Sven and Capuccini,
   Marco and Cascante, Marta and de Atauri, Pedro and Ebbels, Timothy M. D.
   and Foguet, Carles and Glen, Robert and Gonzalez-Beltran, Alejandra and
   Gunther, Ulrich L. and Handakas, Evangelos and Hankemeier, Thomas and
   Haug, Kenneth and Herman, Stephanie and Holub, Petr and Izzo,
   Massimiliano and Jacob, Daniel and Johnson, David and Jourdan, Fabien
   and Kale, Namrata and Karaman, Ibrahim and Khalili, Bita and Khonsari,
   Payam Emami and Kultima, Kim and Lampa, Samuel and Larsson, Anders and
   Ludwig, Christian and Moreno, Pablo and Neumann, Steffen and Novella,
   Jon Ander and O'Donovan, Claire and Pearce, Jake T. M. and Peluso, Alina
   and Piras, Marco Enrico and Pireddu, Luca and Reed, Michelle A. C. and
   Rocca-Serra, Philippe and Roger, Pierrick and Rosato, Antonio and
   Rueedi, Rico and Ruttkies, Christoph and Sadawi, Noureddin and Salek,
   Reza M. and Sansone, Susanna-Assunta and Selivanov, Vitaly and Spjuth,
   Ola and Schober, Daniel and Thevenot, Etienne A. and Tomasoni, Mattia
   and van Rijswijk, Merlijn and van Vliet, Michael and Viant, Mark R. and
   Weber, Ralf J. M. and Zanetti, Gianluigi and Steinbeck, Christoph},
Title = {PhenoMeNal: processing and analysis of metabolomics data in the cloud},
Journal = {GIGASCIENCE},
Year = {2019},
Volume = {8},
Number = {2},
Month = {FEB},
Abstract = {Background Metabolomics is the comprehensive study of a multitude of
   small molecules to gain insight into an organism's metabolism. The
   research field is dynamic and expanding with applications across
   biomedical, biotechnological, and many other applied biological domains.
   Its computationally intensive nature has driven requirements for open
   data formats, data repositories, and data analysis tools. However, the
   rapid progress has resulted in a mosaic of independent, and sometimes
   incompatible, analysis methods that are difficult to connect into a
   useful and complete data analysis solution.
   Findings PhenoMeNal (Phenome and Metabolome aNalysis) is an advanced and
   complete solution to set up Infrastructure-as-a-Service (IaaS) that
   brings workflow-oriented, interoperable metabolomics data analysis
   platforms into the cloud. PhenoMeNal seamlessly integrates a wide array
   of existing open-source tools that are tested and packaged as Docker
   containers through the project's continuous integration process and
   deployed based on a kubernetes orchestration framework. It also provides
   a number of standardized, automated, and published analysis workflows in
   the user interfaces Galaxy, Jupyter, Luigi, and Pachyderm.
   Conclusions PhenoMeNal constitutes a keystone solution in cloud
   e-infrastructures available for metabolomics. PhenoMeNal is a unique and
   complete solution for setting up cloud e-infrastructures through
   easy-to-use web interfaces that can be scaled to any custom public and
   private cloud environment. By harmonizing and automating software
   installation and configuration and through ready-to-use scientific
   workflow user interfaces, PhenoMeNal has succeeded in providing
   scientists with workflow-driven, reproducible, and shareable
   metabolomics data analysis platforms that are interfaced through
   standard data formats, representative datasets, versioned, and have been
   tested for reproducibility and interoperability. The elastic
   implementation of PhenoMeNal further allows easy adaptation of the
   infrastructure to other application areas and omics research domains.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Peters, K (Corresponding Author), Leibniz Inst Plant Biochem, Stress \& Dev Biol, Weinberg 3, D-06120 Halle, Germany.
   Bradbury, J (Corresponding Author), Univ Birmingham, Sch Biosci, Birmingham B15 2TT, W Midlands, England.
   Steinbeck, C (Corresponding Author), Inst Analyt Chem, Cheminformat \& Computat Metabol, Lessingstr 8, D-07743 Jena, Germany.
   Peters, Kristian; Neumann, Steffen; Ruttkies, Christoph; Schober, Daniel, Leibniz Inst Plant Biochem, Stress \& Dev Biol, Weinberg 3, D-06120 Halle, Germany.
   Bradbury, James; Viant, Mark R.; Weber, Ralf J. M., Univ Birmingham, Sch Biosci, Birmingham B15 2TT, W Midlands, England.
   Bergmann, Sven; Khalili, Bita; Rueedi, Rico; Tomasoni, Mattia, Univ Lausanne, Dept Computat Biol, Lausanne, Switzerland.
   Bergmann, Sven; Khalili, Bita; Rueedi, Rico; Tomasoni, Mattia, Swiss Inst Bioinformat, Lausanne, Switzerland.
   Capuccini, Marco, Uppsala Univ, Div Comp Sci, Dept Informat Technol, Uppsala, Sweden.
   Capuccini, Marco; Herman, Stephanie; Lampa, Samuel; Larsson, Anders; Novella, Jon Ander; Spjuth, Ola, Uppsala Univ, Dept Pharmaceut Biosci, Box 591, S-75124 Uppsala, Sweden.
   Cascante, Marta; de Atauri, Pedro; Foguet, Carles; Selivanov, Vitaly, Univ Barcelona, Dept Biochem \& Mol Biomed, Barcelona, Spain.
   Cascante, Marta; de Atauri, Pedro; Foguet, Carles; Selivanov, Vitaly, ISCIII, CIBEREHD, Barcelona, Spain.
   Sadawi, Noureddin, Brunel Univ, Dept Comp Sci, Coll Engn Design \& Phys Sci, London, England.
   Ebbels, Timothy M. D.; Glen, Robert; Handakas, Evangelos; Pearce, Jake T. M.; Peluso, Alina; Sadawi, Noureddin, Imperial Coll London, Dept Surg \& Canc, London SW7 2AZ, England.
   Glen, Robert, Univ Cambridge, Dept Chem, Ctr Mol Informat, Lensfield Rd, Cambridge CB2 1EW, England.
   Gonzalez-Beltran, Alejandra; Izzo, Massimiliano; Johnson, David; Rocca-Serra, Philippe; Sansone, Susanna-Assunta, Univ Oxford, Dept Engn Sci, Oxford E Res Ctr, 7 Keble Rd, Oxford OX1 3QG, England.
   Gunther, Ulrich L.; Reed, Michelle A. C., Univ Birmingham, Inst Canc \& Genom Sci, Birmingham B15 2TT, W Midlands, England.
   van Rijswijk, Merlijn, Netherlands Metabol Ctr, NL-2333 CC Leiden, Netherlands.
   Hankemeier, Thomas; van Vliet, Michael, Leiden Univ, LACDR, Div Syst Biomed \& Pharmacol, NL-2333 CC Leiden, Netherlands.
   Haug, Kenneth; Kale, Namrata; Moreno, Pablo; O'Donovan, Claire; Salek, Reza M., EBI, EMBL, Wellcome Genome Campus, Cambridge CB10 1SD, England.
   Herman, Stephanie; Khonsari, Payam Emami; Kultima, Kim, Uppsala Univ, Clin Chem, Dept Med Sci, S-75185 Uppsala, Sweden.
   Holub, Petr, BBMRI ERIC, Graz, Austria.
   Jacob, Daniel, Univ Bordeaux, INRA, Plateforme Metabolome Bordeaux MetaboHUB, F-33140 Villenave Dornon, France.
   Johnson, David, Uppsala Univ, Dept Informat \& Media, Box 513, S-75120 Uppsala, Sweden.
   Jourdan, Fabien, INRA French Natl Inst Agr Res, UMR1331, Toxalim, Res Ctr Food Toxicol, Toulouse, France.
   Karaman, Ibrahim, Imperial Coll London, Sch Publ Hlth, Dept Epidemiol \& Biostat, St Marys Campus,Norfolk Pl, London W2 1PG, England.
   Larsson, Anders; Novella, Jon Ander, Uppsala Univ, Natl Bioinformat Infrastruct Sweden, Uppsala, Sweden.
   Ludwig, Christian, Univ Birmingham, IMSR, Birmingham B15 2TT, W Midlands, England.
   Neumann, Steffen, German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany.
   Piras, Marco Enrico; Pireddu, Luca; Zanetti, Gianluigi, CRS4, Distributed Comp Grp, Pula, Italy.
   Roger, Pierrick; Thevenot, Etienne A., CEA, LIST, Lab Data Anal \& Syst Intelligence, MetaboHUB, F-91191 Gif Sur Yvette, France.
   Rosato, Antonio, Univ Florence, Magnet Resonance Ctr CERM, I-50019 Florence, Italy.
   Rosato, Antonio, Univ Florence, Dept Chem, I-50019 Florence, Italy.
   Rosato, Antonio, CIRMMP, I-50019 Florence, Italy.
   van Rijswijk, Merlijn, Dutch Techctr Life Sci, ELIXIR NL, NL-3503 RM Utrecht, Netherlands.
   Viant, Mark R.; Weber, Ralf J. M., Univ Birmingham, Phenome Ctr Birmingham, Birmingham B15 2TT, W Midlands, England.
   Steinbeck, Christoph, Inst Analyt Chem, Cheminformat \& Computat Metabol, Lessingstr 8, D-07743 Jena, Germany.},
DOI = {10.1093/gigascience/giy149},
Article-Number = {giy149},
ISSN = {2047-217X},
Keywords = {metabolomics; data analysis; e-infrastructures; NMR; mass spectrometry;
   computational workflows; galaxy; cloud computing; standardization;
   statistics},
Keywords-Plus = {MASS-SPECTROMETRY; STANDARDS; SPECTRA; METABOLITES; PLATFORM; SYSTEM;
   TOOL; INTEGRATION; ANNOTATION; REPOSITORY},
Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Science \& Technology -
   Other Topics},
Web-of-Science-Categories  = {Biology; Multidisciplinary Sciences},
Author-Email = {kpeters@ipb-halle.de
   j.bradbury@bham.ac.uk
   christoph.steinbeck@uni-jena.de},
Affiliations = {Leibniz Institut fur Pflanzenbiochemie; University of Birmingham;
   University of Lausanne; Swiss Institute of Bioinformatics; Uppsala
   University; Uppsala University; University of Barcelona; Instituto de
   Salud Carlos III; CIBER - Centro de Investigacion Biomedica en Red;
   CIBEREHD; Brunel University; Imperial College London; University of
   Cambridge; University of Oxford; University of Birmingham; Leiden
   University - Excl LUMC; Leiden University; European Molecular Biology
   Laboratory (EMBL); Uppsala University; Universite de Bordeaux; INRAE;
   Uppsala University; INRAE; Universite de Toulouse; Universite Toulouse
   III - Paul Sabatier; Universite Federale Toulouse Midi-Pyrenees (ComUE);
   Institut National Polytechnique de Toulouse; Imperial College London;
   Uppsala University; University of Birmingham; Universite Paris Saclay;
   CEA; University of Florence; University of Florence; University of
   Birmingham},
ResearcherID-Numbers = {Rosato, Antonio/M-3250-2019
   de Atauri, Pedro/AAG-2384-2020
   Spjuth, Ola/Q-2638-2019
   Steinbeck, Christoph/B-4131-2008
   Viant, Mark R/B-6339-2009
   Ebbels, Tim/ABB-2627-2021
   Foguet, Carles/W-4864-2018
   Chandakas, Evangelos/AAA-7694-2022
   Jourdan, Fabien/AAW-5075-2021
   CASCANTE, MARTA/AFK-5991-2022
   Salek, Reza/V-9739-2017
   Jacob, Daniel/AAQ-9846-2020
   Lampa, Samuel/L-9673-2019
   de Atauri, Pedro Ramón/R-3957-2019
   Haug, Ove Kenneth/O-3809-2019
   CASCANTE, MARTA/AAG-4355-2022
   Haug, Kenneth/AAD-4241-2019
   Moreno, Pablo/AAC-7057-2020
   Hankemeier, Thomas/V-5407-2019
   Ludwig, Christian/E-7679-2011
   Holub, Petr/A-5848-2015
   Neumann, Steffen/K-5554-2012
   Haug, Ove Kenneth/D-8694-2017
   },
ORCID-Numbers = {Rosato, Antonio/0000-0001-6172-0368
   de Atauri, Pedro/0000-0002-7754-7851
   Spjuth, Ola/0000-0002-8083-2864
   Viant, Mark R/0000-0001-5898-4119
   Ebbels, Tim/0000-0002-3372-8423
   Foguet, Carles/0000-0001-8494-9595
   Chandakas, Evangelos/0000-0002-9291-9641
   Jourdan, Fabien/0000-0001-9401-2894
   CASCANTE, MARTA/0000-0002-2062-4633
   Salek, Reza/0000-0001-8604-1732
   Jacob, Daniel/0000-0002-6687-7169
   Lampa, Samuel/0000-0001-6740-9212
   de Atauri, Pedro Ramón/0000-0002-7754-7851
   CASCANTE, MARTA/0000-0002-2062-4633
   Moreno, Pablo/0000-0002-9856-1679
   Hankemeier, Thomas/0000-0001-7871-2073
   Ludwig, Christian/0000-0001-8901-6970
   Holub, Petr/0000-0002-5358-616X
   Neumann, Steffen/0000-0002-7899-7192
   Pireddu, Luca/0000-0002-4663-5613
   Izzo, Massimiliano/0000-0002-8100-6142
   Steinbeck, Christoph/0000-0001-6966-0814
   Haug, Ove Kenneth/0000-0003-3168-4145
   Roger, Pierrick/0000-0001-8177-4873
   Peters, Kristian/0000-0002-4321-0257
   Kultima, Kim/0000-0002-0680-1410
   Glen, Robert/0000-0003-1759-2914
   Emami Khoonsari, Payam/0000-0002-4137-5517
   Pearce, Jake/0000-0003-4637-3171
   Karaman, Ibrahim/0000-0001-9341-8155
   Tomasoni, Mattia/0000-0001-8775-2384
   Johnson, David/0000-0002-2323-6847
   Gonzalez-Beltran, Alejandra/0000-0003-3499-8262
   Sadawi, Noureddin/0000-0002-2195-8264
   Thevenot, Etienne A./0000-0003-1019-4577
   Schober, Daniel/0000-0001-8014-6648
   O'Donovan, Claire/0000-0001-8051-7429
   Novella, Jon Ander/0000-0002-2187-5426},
Funding-Acknowledgement = {European Commission PhenoMeNal {[}EC654241]; BBSRC {[}BB/J020265/1,
   BB/H024921/1, BB/I000771/1, BB/M027635/1, BB/L024101/1] Funding Source:
   UKRI},
Funding-Text = {The project was funded by the European Commission PhenoMeNal (grant
   EC654241). The consortium members include J.B., M.Cap., M. Cas., P.dA.,
   T.M.D.E., R.G., A.G.-B., K.H., M.I., D.Jo., F.J., N.K., P.E.K., A.L.,
   P.M., S.N., C.O.D., K.P., L.P., M.A.C.R., P.R.-S., P.R.M., A.R., R.R.,
   C.R., T.H., M.vR., M.vV., N.S., R.M.S., S.-A.S., D.S., O.S., V.S.,
   E.A.T., M.T., M.R.V., and R.J.M.W. C.S. received funding from the
   European Commission PhenoMeNal (grant EC654241).},
Number-of-Cited-References = {96},
Times-Cited = {48},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {23},
Journal-ISO = {GigaScience},
Doc-Delivery-Number = {HQ6TT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000462551600002},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000667549500028,
Author = {Kakalia, Zarine and Varadharajan, Charuleka and Alper, Erek and Brodie,
   Eoin L. and Burrus, Madison and Carroll, Rosemary W. H. and
   Christianson, Danielle S. and Dong, Wenming and Hendrix, Valerie C. and
   Henderson, Matthew and Hubbard, Susan S. and Johnson, Douglas and
   Versteeg, Roelof and Williams, Kenneth H. and Agarwal, Deborah A.},
Title = {The Colorado East River Community Observatory Data Collection},
Journal = {HYDROLOGICAL PROCESSES},
Year = {2021},
Volume = {35},
Number = {6},
Month = {JUN},
Abstract = {The U.S. Department of Energy's (DOE) Colorado East River Community
   Observatory (ER) in the Upper Colorado River Basin was established in
   2015 as a representative mountainous, snow-dominated watershed to study
   hydrobiogeochemical responses to hydrological perturbations in headwater
   systems. The ER is characterized by steep elevation, geologic,
   hydrologic and vegetation gradients along floodplain, montane,
   subalpine, and alpine life zones, which makes it an ideal location for
   researchers to understand how different mountain subsystems contribute
   to overall watershed behaviour. The ER has both long-term and
   spatially-extensive observations and experimental campaigns carried out
   by the Watershed Function Scientific Focus Area (SFA), led by Lawrence
   Berkeley National Laboratory, and researchers from over 30 organizations
   who conduct cross-disciplinary process-based investigations and
   modelling of watershed behaviour. The heterogeneous data generated at
   the ER include hydrological, genomic, biogeochemical, climate,
   vegetation, geological, and remote sensing data, which combined with
   model inputs and outputs comprise a collection of datasets and
   value-added products within a mountainous watershed that span multiple
   spatiotemporal scales, compartments, and life zones. Within 5 years of
   collection, these datasets have revealed insights into numerous aspects
   of watershed function such as factors influencing snow accumulation and
   melt timing, water balance partitioning, and impacts of floodplain
   biogeochemistry and hillslope ecohydrology on riverine geochemical
   exports. Data generated by the SFA are managed and curated through its
   Data Management Framework. The SFA has an open data policy, and over 70
   ER datasets are publicly available through relevant data repositories. A
   public interactive map of data collection sites run by the SFA is
   available to inform the broader community about SFA field activities.
   Here, we describe the ER and the SFA measurement network, present the
   public data collection generated by the SFA and partner institutions,
   and highlight the value of collecting multidisciplinary multiscale
   measurements in representative catchment observatories.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Varadharajan, C (Corresponding Author), Lawrence Berkeley Natl Lab, Earth \& Environm Sci Area, 1 Cyclotron Rd,84-142 M-S 74R316C, Berkeley, CA 94720 USA.
   Kakalia, Zarine; Varadharajan, Charuleka; Brodie, Eoin L.; Burrus, Madison; Dong, Wenming; Hubbard, Susan S.; Williams, Kenneth H., Lawrence Berkeley Natl Lab, Earth \& Environm Sci Area, 1 Cyclotron Rd,84-142 M-S 74R316C, Berkeley, CA 94720 USA.
   Kakalia, Zarine; Johnson, Douglas; Versteeg, Roelof, Univ Calif Berkeley, Coll Nat Resources, Berkeley, CA 94720 USA.
   Alper, Erek, Subsurface Insights LLC, Hanover, NH USA.
   Carroll, Rosemary W. H.; Hendrix, Valerie C.; Henderson, Matthew; Agarwal, Deborah A., Desert Res Inst, Div Hydrol Sci, Reno, NV USA.
   Christianson, Danielle S., Lawrence Berkeley Natl Lab, Comp Sci Area, Berkeley, CA USA.},
DOI = {10.1002/hyp.14243},
Article-Number = {e14243},
ISSN = {0885-6087},
EISSN = {1099-1085},
Keywords = {diverse watershed data; East River; hydrobiogeochemical processes;
   mountainous watershed observatory; watershed function science focus
   area; watershed function SFA data},
Research-Areas = {Water Resources},
Web-of-Science-Categories  = {Water Resources},
Author-Email = {cvaradharajan@lbl.gov},
Affiliations = {United States Department of Energy (DOE); Lawrence Berkeley National
   Laboratory; University of California System; University of California
   Berkeley; Nevada System of Higher Education (NSHE); Desert Research
   Institute NSHE; United States Department of Energy (DOE); Lawrence
   Berkeley National Laboratory},
ResearcherID-Numbers = {Varadharajan, Charuleka/S-4238-2019
   Dong, Wenming/G-3221-2015
   Varadharajan, Charuleka/G-3741-2015
   Williams, Kenneth Hurst/O-5181-2014
   Versteeg, Roelof/JKH-8378-2023
   Brodie, Eoin L/A-7853-2008
   Hubbard, Susan S/E-9508-2010
   },
ORCID-Numbers = {Varadharajan, Charuleka/0000-0002-4142-3224
   Dong, Wenming/0000-0003-2074-8887
   Varadharajan, Charuleka/0000-0002-4142-3224
   Williams, Kenneth Hurst/0000-0002-3568-1155
   Brodie, Eoin L/0000-0002-8453-8435
   Hubbard, Susan S/0000-0003-2966-5631
   Christianson, Danielle/0000-0002-8663-7701
   Hendrix, Valerie C./0000-0001-9061-8952},
Funding-Acknowledgement = {Biological and Environmental Research; Office of Science; U.S.
   Department of Energy},
Funding-Text = {Biological and Environmental Research; Office of Science; U.S.
   Department of Energy},
Number-of-Cited-References = {89},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Hydrol. Process.},
Doc-Delivery-Number = {TA9EZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000667549500028},
OA = {Green Published, hybrid, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000345810000016,
Author = {Poelen, Jorrit H. and Simons, James D. and Mungall, Chris J.},
Title = {Global biotic interactions: An open infrastructure to share and analyze
   species-interaction datasets},
Journal = {ECOLOGICAL INFORMATICS},
Year = {2014},
Volume = {24},
Pages = {148-159},
Month = {NOV},
Abstract = {An intricate network of interactions between organisms and their
   environment form the ecosystems that sustain life on earth. With a
   detailed understanding of these interactions, ecologists and biologists
   can make better informed predictions about the ways different
   environmental factors will impact ecosystems. Despite the abundance of
   research data on biotic and abiotic interactions, no comprehensive and
   easily accessible data collection is available that spans taxonomic,
   geospatial, and temporal domains. Biotic-interaction datasets are
   effectively siloed, inhibiting cross-dataset comparisons. In order to
   pool resources and bring to light individual datasets, specialized
   research tools are needed to aggregate, normalize, and integrate
   existing datasets with standard taxonomies, ontologies, vocabularies,
   and structured data repositories. Global Biotic Interactions (GloBI)
   provides such tools by way of an open, community-driven infrastructure
   designed to lower the barrier for researchers to perform ecological
   systems analysis and modeling. GloBI provides a tool that (a) ingests,
   normalizes, and aggregates datasets, (b) integrates interoperable data
   with accepted ontologies (e.g., OBO Relations Ontology, Uberon, and
   Environment Ontology), vocabularies (e.g., Coastal and Marine Ecological
   Classification Standard), and taxonomies (e.g., Integrated Taxonomic
   Information System and National Center for Biotechnology Information
   Taxonomy Database), (c) makes data accessible through an application
   programming interface (API) and various data archives (Darwin Core,
   Turtle, and Neo4j), and (d) houses a data collection of about 700,000
   species interactions across about 50,000 taxa, covering over 1100
   references from 19 data sources. GloBI has taken an open-source and
   open-data approach in order to make integrated species-interaction data
   maximally accessible and to encourage users to provide feedback,
   contribute data, and improve data access methods. The GloBI collection
   of datasets is currently used in the Encyclopedia of Life (EOL) and Gulf
   of Mexico Species Interactions (GoMexSI). (C) 2014 The Authors.
   Published by Elsevier B.V.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Poelen, JH (Corresponding Author), 400 Perkins St,Apt 104, Oakland, CA 94610 USA.
   Simons, James D., Ctr Coastal Studies, Nat Resource Ctr, Corpus Christi, TX 78412 USA.
   Mungall, Chris J., Univ Calif Berkeley, Lawrence Berkeley Natl Lab, Genom Div, Berkeley, CA 94720 USA.},
DOI = {10.1016/j.ecoinf.2014.08.005},
ISSN = {1574-9541},
EISSN = {1878-0512},
Keywords = {Species interactions; Data integration; Taxonomy; Ontology},
Keywords-Plus = {ECOREGIONS; VISUALIZATION; BIODIVERSITY; ENVIRONMENT; NETWORKS; SYSTEM;
   WORLD; LIFE; MAP},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {jhpoelen@xs4all.nl},
Affiliations = {University of California System; University of California Berkeley;
   United States Department of Energy (DOE); Lawrence Berkeley National
   Laboratory},
ResearcherID-Numbers = {Mungall, Chris/I-6006-2019
   },
ORCID-Numbers = {Mungall, Chris/0000-0002-6601-2165
   Poelen, Jorrit/0000-0003-3138-4118},
Funding-Acknowledgement = {Encyclopedia of Life, EOL Rubenstein Fellows Program; David M.
   Rubenstein Grant (CRDF), Smithsonian Institution {[}EOL-33066-13/F33066]},
Funding-Text = {We thank Jen Hammock, Brian Hayden, Peter Roopnarine, Jeff Holmes, and
   Cyndy Parr for sharing their ideas, participating in discussions, and
   supporting our efforts. Also, thanks to Robert Reiz, Goran Bodenschatz,
   Stephan Gosnell, and Sergey Slyusarev for using and providing feedback
   on GloBI data as part of developing software and visualizations. Thanks
   to Pepper Luboff for editing this article. Last but not least, we thank
   all the data contributors that have opened up their datasets and
   answered many of our questions: Malcolm Storey; Joel Sachs; Ken-ichi
   Ueda; Allen Hurlbert; Ben Raymond; Carolyn Barnes; Jarrett Byrnes; Colt
   Cook; Jos Ferrer-Paris; Anne Thessen; Institute for Marine Resources and
   Ecosystem Studies (IMARES); International Council for Exploration of the
   Sea (ICES); UK Species Inventory at the Angela Marmont Centre for UK
   Biodiversity, the Natural History Museum, London; and many others. This
   work has been supported by the Encyclopedia of Life, EOL Rubenstein
   Fellows Program and the David M. Rubenstein Grant (CRDF
   EOL-33066-13/F33066), Smithsonian Institution.},
Number-of-Cited-References = {52},
Times-Cited = {121},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {43},
Journal-ISO = {Ecol. Inform.},
Doc-Delivery-Number = {AU7WU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000345810000016},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000312893300114,
Author = {Franceschini, Andrea and Szklarczyk, Damian and Frankild, Sune and Kuhn,
   Michael and Simonovic, Milan and Roth, Alexander and Lin, Jianyi and
   Minguez, Pablo and Bork, Peer and von Mering, Christian and Jensen, Lars
   J.},
Title = {STRING v9.1: protein-protein interaction networks, with increased
   coverage and integration},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2013},
Volume = {41},
Number = {D1},
Pages = {D808-D815},
Month = {JAN},
Abstract = {Complete knowledge of all direct and indirect interactions between
   proteins in a given cell would represent an important milestone towards
   a comprehensive description of cellular mechanisms and functions.
   Although this goal is still elusive, considerable progress has been
   made-particularly for certain model organisms and functional systems.
   Currently, protein interactions and associations are annotated at
   various levels of detail in online resources, ranging from raw data
   repositories to highly formalized pathway databases. For many
   applications, a global view of all the available interaction data is
   desirable, including lower-quality data and/or computational
   predictions. The STRING database (http://string-db.org/) aims to provide
   such a global perspective for as many organisms as feasible. Known and
   predicted associations are scored and integrated, resulting in
   comprehensive protein networks covering > 1100 organisms. Here, we
   describe the update to version 9.1 of STRING, introducing several
   improvements: (i) we extend the automated mining of scientific texts for
   interaction information, to now also include full-text articles; (ii) we
   entirely re-designed the algorithm for transferring interactions from
   one model organism to the other; and (iii) we provide users with
   statistical information on any functional enrichment observed in their
   networks.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {von Mering, C (Corresponding Author), Univ Zurich, Inst Mol Life Sci, CH-8006 Zurich, Switzerland.
   Franceschini, Andrea; Simonovic, Milan; Roth, Alexander; von Mering, Christian, Univ Zurich, Inst Mol Life Sci, CH-8006 Zurich, Switzerland.
   Franceschini, Andrea; Simonovic, Milan; Roth, Alexander; von Mering, Christian, Univ Zurich, Swiss Inst Bioinformat, CH-8006 Zurich, Switzerland.
   Szklarczyk, Damian; Frankild, Sune; Jensen, Lars J., Univ Copenhagen, Novo Nordisk Fdn Ctr Prot Res, DK-1168 Copenhagen, Denmark.
   Kuhn, Michael, Tech Univ Dresden, Ctr Biotechnol, Dresden, Germany.
   Lin, Jianyi, Univ Milan, Dept Comp Sci, I-20122 Milan, Italy.
   Minguez, Pablo; Bork, Peer, European Mol Biol Lab, Heidelberg, Germany.
   Bork, Peer, Max Delbruck Ctr Mol Med, Berlin, Germany.},
DOI = {10.1093/nar/gks1094},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MOLECULAR INTERACTION DATABASE; METABOLIC PATHWAYS; GENES; PREDICTION;
   VISUALIZATION; ENRICHMENT; FAMILIES; TOOLS; LISTS; FOLDS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {bork@embl.de
   mering@imls.uzh.ch
   lars.juhl.jensen@cpr.ku.dk},
Affiliations = {University of Zurich; Swiss Institute of Bioinformatics; University of
   Zurich; University of Copenhagen; Technische Universitat Dresden;
   University of Milan; European Molecular Biology Laboratory (EMBL);
   Helmholtz Association; Max Delbruck Center for Molecular Medicine},
ResearcherID-Numbers = {Lin, Jianyi/AAT-9024-2020
   von Mering, Christian/B-3300-2008
   Franceschini, Andrea/AAE-8362-2019
   von Mering, Christian/AAB-3699-2020
   Lin, Jianyi/G-9130-2015
   Franceschini, Andrea/IAR-0609-2023
   Kuhn, Michael/D-4978-2009
   Bork, Peer/F-1813-2013
   Jensen, Lars Juhl/C-6492-2008
   Minguez, Pablo/D-4822-2013
   },
ORCID-Numbers = {Lin, Jianyi/0000-0002-3299-448X
   von Mering, Christian/0000-0001-7734-9102
   Lin, Jianyi/0000-0002-3299-448X
   Kuhn, Michael/0000-0002-2841-872X
   Bork, Peer/0000-0002-2627-833X
   Jensen, Lars Juhl/0000-0001-7885-715X
   Minguez, Pablo/0000-0003-4099-9421
   Pletscher-Frankild, Sune/0000-0002-7745-193X
   Franceschini, Andrea/0009-0008-7282-6975},
Funding-Acknowledgement = {Swiss Institute of Bioinformatics (SIB); Novo Nordisk Foundation Center
   for Protein Research; European Molecular Biology Laboratory (EMBL);
   University of Zurich; Novo Nordisk Foundation Center for Protein
   Research {[}PI Lars Juhl Jensen] Funding Source: researchfish},
Funding-Text = {The Swiss Institute of Bioinformatics (SIB) provides sustained funding
   for this project. Work on the project has also been supported in part by
   the Novo Nordisk Foundation Center for Protein Research and the European
   Molecular Biology Laboratory (EMBL). Funding for open access charge:
   University of Zurich.},
Number-of-Cited-References = {60},
Times-Cited = {3132},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {47},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {062BE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000312893300114},
OA = {Green Submitted, Green Published, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000298601300160,
Author = {Baker, Erich J. and Jay, Jeremy J. and Bubier, Jason A. and Langston,
   Michael A. and Chesler, Elissa J.},
Title = {GeneWeaver: a web-based system for integrative functional genomics},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2012},
Volume = {40},
Number = {D1},
Pages = {D1067-D1076},
Month = {JAN},
Abstract = {High-throughput genome technologies have produced a wealth of data on
   the association of genes and gene products to biological functions.
   Investigators have discovered value in combining their experimental
   results with published genome-wide association studies, quantitative
   trait locus, microarray, RNA-sequencing and mutant phenotyping studies
   to identify gene-function associations across diverse experiments,
   species, conditions, behaviors or biological processes. These
   experimental results are typically derived from disparate data
   repositories, publication supplements or reconstructions from primary
   data stores. This leaves bench biologists with the complex and
   unscalable task of integrating data by identifying and gathering
   relevant studies, reanalyzing primary data, unifying gene identifiers
   and applying ad hoc computational analysis to the integrated set. The
   freely available GeneWeaver (http://www.GeneWeaver.org) powered by the
   Ontological Discovery Environment is a curated repository of genomic
   experimental results with an accompanying tool set for dynamic
   integration of these data sets, enabling users to interactively address
   questions about sets of biological functions and their relations to sets
   of genes. Thus, large numbers of independently published genomic results
   can be organized into new conceptual frameworks driven by the
   underlying, inferred biological relationships rather than a pre-existing
   semantic framework. An empirical `ontology' is discovered from the
   aggregate of experimental knowledge around user-defined areas of
   biological inquiry.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Chesler, EJ (Corresponding Author), Jackson Lab, 600 Main St, Bar Harbor, ME 04609 USA.
   Jay, Jeremy J.; Bubier, Jason A.; Chesler, Elissa J., Jackson Lab, Bar Harbor, ME 04609 USA.
   Baker, Erich J., Baylor Univ, Sch Engn \& Comp Sci, Waco, TX 76798 USA.
   Langston, Michael A., Univ Tennessee, Dept Elect Engn \& Comp Sci, Knoxville, TN 37996 USA.},
DOI = {10.1093/nar/gkr968},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {DATABASE; INFORMATION; RESOURCE; DISEASE; EXPLORATION; ONTOLOGY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {Elissa.chesler@jax.org},
Affiliations = {Jackson Laboratory; Baylor University; University of Tennessee System;
   University of Tennessee Knoxville},
ResearcherID-Numbers = {Bubier, Jason A./N-9306-2019
   Jay, Jeremy J/H-6063-2011
   Jay, Jeremy/AAV-5143-2020
   Chesler, Elissa/K-4641-2019
   Bubier, Jason/GWB-9896-2022
   Bubier, Jason/GQA-5404-2022
   Langston, Michael A/A-9484-2011},
ORCID-Numbers = {Bubier, Jason A./0000-0001-5013-1234
   Jay, Jeremy J/0000-0002-5761-7533
   Jay, Jeremy/0000-0002-5761-7533
   Chesler, Elissa/0000-0002-5642-5062
   Bubier, Jason/0000-0001-5013-1234
   Bubier, Jason/0000-0001-5013-1234
   },
Funding-Acknowledgement = {National Institutes of Health {[}NIAAA U01 AA13499, RO1 AA18776]; NIH
   {[}RO1 AA18776]},
Funding-Text = {National Institutes of Health (NIAAA U01 AA13499, RO1 AA18776). Early
   development of the Ontological Discovery Environment occurred as a pilot
   of the Integrative Neuroscience Initiative on Alcoholism. Funding for
   open access charge: NIH RO1 AA18776.},
Number-of-Cited-References = {34},
Times-Cited = {82},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {869MD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000298601300160},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000852410300005,
Author = {Sheffield, Nathan C. and Bonazzi, Vivien R. and Bourne, Philip E. and
   Burdett, Tony and Clark, Timothy and Grossman, Robert L. and Spjuth, Ola
   and Yates, Andrew D.},
Title = {From biomedical cloud platforms to microservices: next steps in FAIR
   data and analysis},
Journal = {SCIENTIFIC DATA},
Year = {2022},
Volume = {9},
Number = {1},
Month = {SEP 8},
Abstract = {The biomedical research community is investing heavily in biomedical
   cloud platforms. Cloud computing holds great promise for addressing
   challenges with big data and ensuring reproducibility in biology.
   However, despite their advantages, cloud platforms in and of themselves
   do not automatically support FAIRness. The global push to develop
   biomedical cloud platforms has led to new challenges, including platform
   lock-in, difficulty integrating across platforms, and duplicated effort
   for both users and developers. Here, we argue that these difficulties
   are systemic and emerge from incentives that encourage development
   effort on self-sufficient platforms and data repositories instead of
   interoperable microservices. We argue that many of these issues would be
   alleviated by prioritizing microservices and access to modular data in
   smaller chunks or summarized form. We propose that emphasizing
   modularity and interoperability would lead to a more powerful Unix-like
   ecosystem of web services for biomedical analysis and data retrieval. We
   challenge funders, developers, and researchers to support a vision to
   improve interoperability through microservices as the next generation of
   cloud-based bioinformatics.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Sheffield, NC (Corresponding Author), Univ Virginia, Sch Med, Ctr Publ Hlth Genom, Charlottesville, VA 22908 USA.
   Sheffield, NC (Corresponding Author), Univ Virginia, Sch Data Sci, Charlottesville, VA 22904 USA.
   Sheffield, NC (Corresponding Author), Univ Virginia, Dept Biomed Engn, Sch Med, Charlottesville, VA 22904 USA.
   Sheffield, NC (Corresponding Author), Univ Virginia, Sch Med, Dept Publ Hlth Sci, Charlottesville, VA 22908 USA.
   Sheffield, NC (Corresponding Author), Univ Virginia, Sch Med, Dept Biochem \& Mol Genet, Charlottesville, VA 22908 USA.
   Sheffield, Nathan C., Univ Virginia, Sch Med, Ctr Publ Hlth Genom, Charlottesville, VA 22908 USA.
   Sheffield, Nathan C.; Bourne, Philip E.; Clark, Timothy, Univ Virginia, Sch Data Sci, Charlottesville, VA 22904 USA.
   Sheffield, Nathan C.; Bourne, Philip E., Univ Virginia, Dept Biomed Engn, Sch Med, Charlottesville, VA 22904 USA.
   Sheffield, Nathan C.; Clark, Timothy, Univ Virginia, Sch Med, Dept Publ Hlth Sci, Charlottesville, VA 22908 USA.
   Sheffield, Nathan C., Univ Virginia, Sch Med, Dept Biochem \& Mol Genet, Charlottesville, VA 22908 USA.
   Bonazzi, Vivien R., Deloitte, Baltimore, MD 20201 USA.
   Burdett, Tony; Yates, Andrew D., European Bioinformat Inst, European Mol Biol Lab, Wellcome Genome Campus, Cambridge CB10 1SD, England.
   Grossman, Robert L., Univ Chicago, Ctr Translat Data Sci, Chicago, IL 60615 USA.
   Spjuth, Ola, Uppsala Univ, Dept Pharmaceut Biosci, S-75124 Uppsala, Sweden.
   Spjuth, Ola, Uppsala Univ, Sci Life Lab, S-75124 Uppsala, Sweden.},
DOI = {10.1038/s41597-022-01619-5},
Article-Number = {553},
EISSN = {2052-4463},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {nsheffield@virginia.edu},
Affiliations = {University of Virginia; University of Virginia; University of Virginia;
   University of Virginia; University of Virginia; Deloitte Touche Tohmatsu
   Limited; European Molecular Biology Laboratory (EMBL); University of
   Chicago; Uppsala University; Uppsala University},
ResearcherID-Numbers = {Bourne, Philip/ABG-8967-2021
   Grossman, Robert/B-1865-2009
   },
ORCID-Numbers = {Bourne, Philip/0000-0002-7618-7292
   Grossman, Robert/0000-0003-3741-5739
   Spjuth, Ola/0000-0002-8083-2864
   Burdett, Anthony/0000-0002-2513-5396
   Clark, Timothy/0000-0003-4060-7360
   Yates, Andrew/0000-0002-8886-4772},
Funding-Acknowledgement = {National Institutes of Health Institute for General Medical Sciences
   (NIGMS) {[}R35GM128636]; European Molecular Biology Laboratory; Wellcome
   Trust {[}WT108749/Z/15/Z]},
Funding-Text = {This work is funded by the National Institutes of Health Institute for
   General Medical Sciences (NIGMS) award R35GM128636 to NCS. PEB is funded
   by an endowment from Scott and Beth Stephenson. ADY and TB are supported
   by the European Molecular Biology Laboratory and ADY by the Wellcome
   Trust (grant number WT108749/Z/15/Z). For open access, we apply a CC BY
   public copyright license to any Author Accepted Manuscript version
   arising from this submission.},
Number-of-Cited-References = {39},
Times-Cited = {3},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Sci. Data},
Doc-Delivery-Number = {4L1QR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000852410300005},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000336095100007,
Author = {Jones, Philip and Binns, David and Chang, Hsin-Yu and Fraser, Matthew
   and Li, Weizhong and McAnulla, Craig and McWilliam, Hamish and Maslen,
   John and Mitchell, Alex and Nuka, Gift and Pesseat, Sebastien and Quinn,
   Antony F. and Sangrador-Vegas, Amaia and Scheremetjew, Maxim and Yong,
   Siew-Yit and Lopez, Rodrigo and Hunter, Sarah},
Title = {InterProScan 5: genome-scale protein function classification},
Journal = {BIOINFORMATICS},
Year = {2014},
Volume = {30},
Number = {9},
Pages = {1236-1240},
Month = {MAY 1},
Abstract = {Motivation: Robust large-scale sequence analysis is a major challenge in
   modern genomic science, where biologists are frequently trying to
   characterize many millions of sequences. Here, we describe a new
   Java-based architecture for the widely used protein function prediction
   software package InterProScan. Developments include improvements and
   additions to the outputs of the software and the complete
   reimplementation of the software framework, resulting in a flexible and
   stable system that is able to use both multiprocessor machines and/or
   conventional clusters to achieve scalable distributed data analysis.
   InterProScan is freely available for download from the EMBl-EBI FTP site
   and the open source code is hosted at Google Code.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Mitchell, A (Corresponding Author), European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Hinxton CB10 1SD, England.
   Jones, Philip; Binns, David; Chang, Hsin-Yu; Fraser, Matthew; Li, Weizhong; McAnulla, Craig; McWilliam, Hamish; Maslen, John; Mitchell, Alex; Nuka, Gift; Pesseat, Sebastien; Quinn, Antony F.; Sangrador-Vegas, Amaia; Scheremetjew, Maxim; Yong, Siew-Yit; Lopez, Rodrigo; Hunter, Sarah, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Hinxton CB10 1SD, England.
   Jones, Philip; Maslen, John, Wellcome Trust Sanger Inst, Hinxton CB10 1SA, England.},
DOI = {10.1093/bioinformatics/btu031},
ISSN = {1367-4803},
EISSN = {1367-4811},
Keywords-Plus = {FAMILY CLASSIFICATION; ANNOTATION; TOPOLOGY},
Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
   Microbiology; Computer Science; Mathematical \& Computational Biology;
   Mathematics},
Web-of-Science-Categories  = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
   Computer Science, Interdisciplinary Applications; Mathematical \&
   Computational Biology; Statistics \& Probability},
Author-Email = {mitchell@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL); Wellcome Trust Sanger
   Institute},
ResearcherID-Numbers = {McWilliam, Hamish/M-5415-2015
   Lopez, Rodrigo/AAC-6111-2019
   },
ORCID-Numbers = {McWilliam, Hamish/0000-0003-1769-5032
   Lopez, Rodrigo/0000-0003-1256-7306
   Fraser, Matthew/0000-0003-2318-9080
   Yong, Siew Yit/0000-0002-1952-3528
   Hunter, Sarah/0000-0003-2453-0770
   Mitchell, Alex/0000-0001-8655-7966
   Sangrador, Amaia/0000-0001-6688-429X
   Scheremetjew, Maxim/0000-0002-7458-3072
   Chang, Hsin Yu/0000-0001-5577-2356
   Li, Weizhong/0000-0002-9003-7733
   Quinn, Antony/0000-0002-0596-7638
   Pesseat, Sebastien/0000-0003-3245-7921},
Funding-Acknowledgement = {Biotechnology and Biological Sciences Research Council (Bioinformatics
   and Biological Resources Fund) {[}BB/ F010508/1]; European Union (under
   the program `FP7 capacities: Scientific Data Repositories') {[}213037];
   Biotechnology and Biological Sciences Research Council {[}BB/F010508/1]
   Funding Source: researchfish; BBSRC {[}BB/F010508/1] Funding Source:
   UKRI},
Funding-Text = {Biotechnology and Biological Sciences Research Council (Bioinformatics
   and Biological Resources Fund) (BB/ F010508/1); European Union (under
   the program `FP7 capacities: Scientific Data Repositories') (213037).
   Open access charges are paid for by EMBL.},
Number-of-Cited-References = {26},
Times-Cited = {4483},
Usage-Count-Last-180-days = {18},
Usage-Count-Since-2013 = {266},
Journal-ISO = {Bioinformatics},
Doc-Delivery-Number = {AH4KE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000336095100007},
OA = {Green Published, hybrid, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000471116800280,
Author = {Rousham, Emily K. and Islam, Mohammad Aminul and Nahar, Papreen and
   Lucas, Patricia Jane and Naher, Nahitun and Ahmed, Syed Masud and
   Nizame, Fosiul Alam and Unicomb, Leanne},
Title = {Pathways of antibiotic use in Bangladesh: qualitative protocol for the
   PAUSE study},
Journal = {BMJ OPEN},
Year = {2019},
Volume = {9},
Number = {1},
Month = {JUN},
Abstract = {Introduction Global actions to reduce antimicrobial resistance (AMR)
   include optimising the use of antimicrobial medicines in human and
   animal health. In countries with weak healthcare regulation, this
   requires a greater understanding of the drivers of antibiotic use from
   the perspective of providers and consumers. In Bangladesh, there is
   limited research on household decision-making and healthcare seeking in
   relation to antibiotic use and consumption for humans and livestock.
   Knowledge is similarly lacking on factors influencing the supply and
   demand for antibiotics among qualified and unqualified healthcare
   providers. The aim of this study is to conduct integrated research on
   household decision-making for healthcare and antibiotic use, as well as
   the awareness, behaviours and priorities of healthcare providers and
   sellers of antibiotics to translate into policy development and
   implementation.
   Methods and analysis In-depth interviews will be conducted with (1)
   household members responsible for decision-making about illness and
   antibiotic use for family and livestock; (2) qualified and unqualified
   private and government healthcare providers in human and animal medicine
   and (3) stakeholders and policy-makers as key informants on the
   development and implementation of policy around AMR. Participant
   observation within retail drug shops will also be carried out.
   Qualitative methods will include a thematic framework analysis. A
   holistic approach to understanding who makes decisions on the sale and
   use of antibiotics, and what drives healthcare seeking in Bangladesh
   will enable identification of routes to behavioural change and the
   development of effective interventions to reduce the health risks of
   AMR.
   Ethics and dissemination Approval for the study has been obtained from
   the Institutional Review Board at the International Centre for
   Diarrhoeal Disease Research, Bangladesh following review by the Research
   and Ethics Committees (PR-16100) and from Loughborough University
   (R17-P081). Information about the study will be provided in a
   participant information letter in Bangla (to be read verbally and given
   in writing to participants). A written informed consent form in Bangla
   will be obtained and participants will be informed of their right to
   withdraw from the study. Dissemination will take place through a 1 day
   dissemination workshop with key stakeholders in public health and
   policy, practitioners and scientists in Bangladesh, and through
   international conference presentations and peer-review publications.
   Anonymised transcripts of interviews will be made available through open
   access via institutional data repositories after an embargo period.},
Publisher = {BMJ PUBLISHING GROUP},
Address = {BRITISH MED ASSOC HOUSE, TAVISTOCK SQUARE, LONDON WC1H 9JR, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Rousham, EK (Corresponding Author), Loughborough Univ, Ctr Global Hlth \& Human Dev, Sch Sport Exercise \& Hlth Sci, Loughborough, Leics, England.
   Rousham, Emily K., Loughborough Univ, Ctr Global Hlth \& Human Dev, Sch Sport Exercise \& Hlth Sci, Loughborough, Leics, England.
   Islam, Mohammad Aminul, Int Ctr Diarrhoeal Dis Res, Lab Sci \& Serv Div, Dhaka, Bangladesh.
   Islam, Mohammad Aminul, Washington State Univ, Paul G Allen Sch Global Anim Hlth, Pullman, WA 99164 USA.
   Nahar, Papreen, Univ Durham, Dept Anthropol, Durham, England.
   Nahar, Papreen, Sussex Univ, Dept Primary Care \& Publ Hlth, Brighton \& Sussex Med Sch, Brighton, E Sussex, England.
   Lucas, Patricia Jane, Univ Bristol, Sch Policy Studies, Bristol, Avon, England.
   Naher, Nahitun; Ahmed, Syed Masud, BRAC Univ, BRAC James P Grant Sch Publ Hlth, Dhaka, Bangladesh.
   Nizame, Fosiul Alam; Unicomb, Leanne, Int Ctr Diarrhoeal Dis Res, Infect Dis Div, Dhaka, Bangladesh.},
DOI = {10.1136/bmjopen-2018-028215},
Article-Number = {e028215},
ISSN = {2044-6055},
Keywords-Plus = {TRANSLATION; INTERVIEWS; PROVIDERS; LANGUAGE; CONTEXT; CALL},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {e.k.rousham@lboro.ac.uk},
Affiliations = {Loughborough University; International Centre for Diarrhoeal Disease
   Research (ICDDR); Washington State University; Durham University;
   University of Sussex; University of Brighton; University of Bristol;
   Bangladesh Rural Advancement Committee BRAC; BRAC University;
   International Centre for Diarrhoeal Disease Research (ICDDR)},
ResearcherID-Numbers = {Ahmed, Syed Masud/AGQ-4786-2022
   Unicomb, Leanne Elizabeth/AAW-4900-2021
   Lucas, Patricia/HNJ-0065-2023
   Ahmed, Syed/GSN-7305-2022
   },
ORCID-Numbers = {Ahmed, Syed Masud/0000-0001-5032-7181
   Unicomb, Leanne Elizabeth/0000-0002-7757-5641
   Rousham, Emily/0000-0001-5654-9279
   Nahar, Papreen/0000-0002-5817-8093
   Lucas, Patricia Jane/0000-0002-0469-8085
   Islam, Mohammad Aminul/0000-0001-5107-5289},
Funding-Acknowledgement = {Antimicrobial Resistance Cross-Council Initiative; Department of Health;
   Department of Environment Food and Rural Affairs; Global Challenges
   Research Fund {[}ES/P004563/1]; ESRC {[}ES/P004563/1] Funding Source:
   UKRI},
Funding-Text = {This work was supported by the Antimicrobial Resistance Cross-Council
   Initiative supported by the seven research councils in partnership with
   the Department of Health, the Department of Environment Food and Rural
   Affairs and the Global Challenges Research Fund (ES/P004563/1).},
Number-of-Cited-References = {30},
Times-Cited = {21},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {BMJ Open},
Doc-Delivery-Number = {IC6XU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000471116800280},
OA = {Green Published, gold, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000640473700006,
Author = {Agarwal, Deborah A. and Damerow, Joan and Varadharajan, Charuleka and
   Christianson, Danielle S. and Pastorello, Gilberto Z. and Cheah, You-Wei
   and Ramakrishnan, Lavanya},
Title = {Balancing the needs of consumers and producers for scientific data
   collections},
Journal = {ECOLOGICAL INFORMATICS},
Year = {2021},
Volume = {62},
Month = {MAY},
Abstract = {Recent emphasis and requirements for open data publication have led to
   significant increases in data availability in the Earth sciences, which
   is critical to long-tail data integration. Currently, data are often
   published in a repository with an identifier and citation, similar to
   those for papers. Subsequent publications that use the data are expected
   to provide a citation in the reference section of the paper. However,
   the format of the data citation is still evolving, particularly with
   regards to citing dynamic data, subsets, and collections of data.
   Considering the motivations of both data producers and consumers, the
   most pressing need is to create userfriendly solutions that provide
   credit for data producers and enable accurate citation of data,
   particularly integrated data. Providing easy-to-use data citations is a
   critical foundation that is required to address the socio-technical
   challenges around data integration. Studies that integrate data from
   dozens or hundreds of datasets must often include data citations in
   supplementary material due to page limits. However, citations in the
   supplementary material are not indexed, making it difficult to track
   citations and thus giving credit to the data producer. In this paper, we
   discuss our experiences and the challenges we have encountered with
   current citation guidance. We also review the relative merits of the
   currently available mechanisms designed to enable compact citation of
   collections of data, such as data collections, data papers, and dynamic
   data citations. We consider these options for three data producer
   scenarios: a domain-specific data collection, a data repository, and a
   large-scale, multidisciplinary project. We posit that a new mechanism is
   also needed to enable citation of multiple datasets and credit to data
   producers.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Agarwal, DA (Corresponding Author), Ernest Orlando Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.
   Agarwal, Deborah A.; Damerow, Joan; Varadharajan, Charuleka; Christianson, Danielle S.; Pastorello, Gilberto Z.; Cheah, You-Wei; Ramakrishnan, Lavanya, Ernest Orlando Lawrence Berkeley Natl Lab, Berkeley, CA 94720 USA.},
DOI = {10.1016/j.ecoinf.2021.101251},
EarlyAccessDate = {MAR 2021},
Article-Number = {101251},
ISSN = {1574-9541},
EISSN = {1878-0512},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {daagarwal@lbl.gov},
Affiliations = {United States Department of Energy (DOE); Lawrence Berkeley National
   Laboratory},
ResearcherID-Numbers = {Pastorello, Gilberto Z/N-8395-2015
   Varadharajan, Charuleka/G-3741-2015
   Varadharajan, Charuleka/S-4238-2019
   Ball-Damerow, Joan/X-7925-2018
   },
ORCID-Numbers = {Pastorello, Gilberto Z/0000-0002-9387-3702
   Varadharajan, Charuleka/0000-0002-4142-3224
   Varadharajan, Charuleka/0000-0002-4142-3224
   Ball-Damerow, Joan/0000-0003-2601-5043
   Agarwal, Deborah/0000-0001-5045-2396},
Funding-Acknowledgement = {AmeriFlux Management Project; U.S. DOE's Office of Science Biological
   and Environmental Research {[}DE-AC02-05CH11231]},
Funding-Text = {We want to thank the members of the ESS-DIVE, AmeriFlux, FLUXNET,
   Watershed Function SFA, and NGEE-Tropics for the many useful discussions
   about citations and credit. We also thank all those who contributed to a
   variety of community discussions on data citations through a variety of
   means and community meetings. We want to particularly thank Shelley
   Stall, Peter Fox, and Martin Fenner for being willing to act as sounding
   boards for citation topics. This work was funded through the AmeriFlux
   Management Project and the ESS-DIVE repository by the U.S. DOE's Office
   of Science Biological and Environmental Research under contract number
   DE-AC02-05CH11231 to LBNL as part of its Earth and Environmental Systems
   Science Division Data Management program.},
Number-of-Cited-References = {45},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Ecol. Inform.},
Doc-Delivery-Number = {RN6PQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000640473700006},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000276399100081,
Author = {Koh, Judice L. Y. and Ding, Huiming and Costanzo, Michael and
   Baryshnikova, Anastasia and Toufighi, Kiana and Bader, Gary D. and
   Myers, Chad L. and Andrews, Brenda J. and Boone, Charles},
Title = {DRYGIN: a database of quantitative genetic interaction networks in yeast},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2010},
Volume = {38},
Number = {1},
Pages = {D502-D507},
Month = {JAN},
Abstract = {Genetic interactions are highly informative for deciphering the
   underlying functional principles that govern how genes control cell
   processes. Recent developments in Synthetic Genetic Array (SGA) analysis
   enable the mapping of quantitative genetic interactions on a genome-wide
   scale. To facilitate access to this resource, which will ultimately
   represent a complete genetic interaction network for a eukaryotic cell,
   we developed DRYGIN (Data Repository of Yeast Genetic Interactions)-a
   web database system that aims at providing a central platform for yeast
   genetic network analysis and visualization. In addition to providing an
   interface for searching the SGA genetic interactions, DRYGIN also
   integrates other data sources, in order to associate the genetic
   interactions with pathway information, protein complexes, other binary
   genetic and physical interactions, and Gene Ontology functional
   annotation. DRYGIN version 1.0 currently holds more than 5.4 million
   measurements of genetic interacting pairs involving similar to 4500
   genes, and is available at http://drygin.ccbr.utoronto.ca},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Koh, JLY (Corresponding Author), Univ Toronto, Banting \& Best Dept Med Res, Terrence Donnelly Ctr Cellular \& Biomol Res, 160 Coll St, Toronto, ON M5S 3E1, Canada.
   Koh, Judice L. Y.; Ding, Huiming; Costanzo, Michael; Baryshnikova, Anastasia; Toufighi, Kiana; Bader, Gary D.; Andrews, Brenda J.; Boone, Charles, Univ Toronto, Banting \& Best Dept Med Res, Terrence Donnelly Ctr Cellular \& Biomol Res, Toronto, ON M5S 3E1, Canada.
   Koh, Judice L. Y.; Ding, Huiming; Costanzo, Michael; Baryshnikova, Anastasia; Toufighi, Kiana; Bader, Gary D.; Andrews, Brenda J.; Boone, Charles, Univ Toronto, Dept Mol Genet, Terrence Donnelly Ctr Cellular \& Biomol Res, Toronto, ON M5S 3E1, Canada.
   Myers, Chad L., Univ Minnesota, Dept Comp Sci \& Engn, Minneapolis, MN 55455 USA.},
DOI = {10.1093/nar/gkp820},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENOME},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {judice.koh@utoronto.ca
   charlie.boone@utoronto.ca},
Affiliations = {University of Toronto; University of Toronto; University of Minnesota
   System; University of Minnesota Twin Cities},
ResearcherID-Numbers = {Ｂｏｏｎｅ, Ｃｈａｒｌｅｓ/IQX-0075-2023
   Bader, Gary/C-1176-2009},
ORCID-Numbers = {Bader, Gary/0000-0003-0185-8861},
Funding-Acknowledgement = {Genome Canada through the Ontario Genomics Institute {[}2004-OGI-3-01]},
Funding-Text = {Genome Canada through the Ontario Genomics Institute {[}2004-OGI-3-01 to
   J. L. Y. K., H. D., M. C., A. B., K. T., G. D. B., B. J. A., C. B.].
   Funding for open access charge: Genome Canada through the Ontario
   Genomics Institute as per research agreement 2004-OGI-3-01.},
Number-of-Cited-References = {19},
Times-Cited = {65},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {579TV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000276399100081},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000772869400001,
Author = {Heather, James M. and Spindler, Matthew J. and Alonso, Marta Herrero and
   Shui, Yifang Ivana and Millar, David G. and Johnson, David S. and
   Cobbold, Mark and Hata, Aaron N.},
Title = {Stitchr: stitching coding TCR nucleotide sequences from V/J/CDR3
   information},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2022},
Volume = {50},
Number = {12},
Month = {JUL 8},
Abstract = {The study and manipulation of T cell receptors (TCRs) is central to
   multiple fields across basic and translational immunology research.
   Produced by V(D)J recombination, TCRs are often only recorded in the
   literature and data repositories as a combination of their V and J gene
   symbols, plus their hypervariable CDR3 amino acid sequence. However,
   numerous applications require full-length coding nucleotide sequences.
   Here we present Stitchr, a software tool developed to specifically
   address this limitation. Given minimal V/J/CDR3 information, Stitchr
   produces complete coding sequences representing a fully spliced TCR
   cDNA. Due to its modular design, Stitchr can be used for TCR engineering
   using either published germline or novel/modified variable and constant
   region sequences. Sequences produced by Stitchr were validated by
   synthesizing and transducing TCR sequences into Jurkat cells,
   recapitulating the expected antigen specificity of the parental TCR.
   Using a companion script, Thimble, we demonstrate that Stitchr can
   process a million TCRs in under ten minutes using a standard desktop
   personal computer. By systematizing the production and modification of
   TCR sequences, we propose that Stitchr will increase the speed,
   repeatability, and reproducibility of TCR research. Stitchr is available
   on GitHub.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Heather, JM; Hata, AN (Corresponding Author), Massachusetts Gen Hosp, Canc Ctr, Charlestown, MA 02129 USA.
   Heather, JM; Hata, AN (Corresponding Author), Harvard Med Sch, Dept Med, Boston, MA 02115 USA.
   Heather, James M.; Alonso, Marta Herrero; Shui, Yifang Ivana; Millar, David G.; Cobbold, Mark; Hata, Aaron N., Massachusetts Gen Hosp, Canc Ctr, Charlestown, MA 02129 USA.
   Heather, James M.; Millar, David G.; Cobbold, Mark; Hata, Aaron N., Harvard Med Sch, Dept Med, Boston, MA 02115 USA.
   Spindler, Matthew J.; Johnson, David S., GigaMune Inc, San Francisco, CA USA.},
DOI = {10.1093/nar/gkac190},
EarlyAccessDate = {MAR 2022},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {T-CELL-RECEPTOR; ALPHA-BETA; INFERENCE; DATABASE; IMMUNOGLOBULIN;
   RECOGNITION; EXPRESSION; REACTIVITY; EXCHANGE; IMPROVE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {jheather@mgh.harvard.edu
   ahata@mgh.harvard.edu},
Affiliations = {Harvard University; Massachusetts General Hospital; Harvard University;
   Harvard Medical School},
ResearcherID-Numbers = {Herrero Alonso, Marta/HKE-2107-2023
   },
ORCID-Numbers = {Herrero Alonso, Marta/0000-0001-8030-6007
   Heather, James/0000-0002-1783-5181},
Funding-Acknowledgement = {NIH/NCI {[}R01CA164273, R43CA232942]; NIH/NIAID {[}R43AI12031301]; Emily
   Venanzi Fund for Innovation in Lung Cancer Research; Be a Piece of the
   Solution; Targeting a Cure for Lung Cancer Research Fund at MGH (Boston,
   MA)},
Funding-Text = {\textbackslash{}NIH/NCI {[}R01CA164273]; NIH/NIAID {[}R43AI12031301 to
   D.S.J.]; NIH/NCI {[}R43CA232942 to M.J.S.]; Emily Venanzi Fund for
   Innovation in Lung Cancer Research; Be a Piece of the Solution, and
   Targeting a Cure for Lung Cancer Research Fund at MGH (Boston, MA).
   Funding for open access charge: Emily Venanzi Fund for Innovation in
   Lung Cancer Research.},
Number-of-Cited-References = {80},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {2Y1UB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000772869400001},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000350210400108,
Author = {Shimoyama, Mary and De Pons, Jeff and Hayman, G. Thomas and
   Laulederkind, Stanley J. F. and Liu, Weisong and Nigam, Rajni and Petri,
   Victoria and Smith, Jennifer R. and Tutaj, Marek and Wang, Shur-Jen and
   Worthey, Elizabeth and Dwinell, Melinda and Jacob, Howard},
Title = {The Rat Genome Database 2015: genomic, phenotypic and environmental
   variations and disease},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2015},
Volume = {43},
Number = {D1},
Pages = {D743-D750},
Month = {JAN 28},
Abstract = {The RatGenome Database (RGD, http://rgd.mcw.edu) provides the most
   comprehensive data repository and informatics platform related to the
   laboratory rat, one of the most important model organisms for disease
   studies. RGD maintains and updates datasets for genomic elements such as
   genes, transcripts and increasingly in recent years, sequence
   variations, as well as map positions for multiple assemblies and
   sequence information. Functional annotations for genomic elements are
   curated from published literature, submitted by researchers and
   integrated from other public resources. Complementing the genomic data
   catalogs are those associated with phenotypes and disease, including
   strains, QTL and experimental phenotype measurements across hundreds of
   strains. Data are submitted by researchers, acquired through bulk data
   pipelines or curated from published literature. Innovative software
   tools provide users with an integrated platform to query, mine, display
   and analyze valuable genomic and phenomic datasets for discovery and
   enhancement of their own research. This update highlights recent
   developments that reflect an increasing focus on: (i) genomic variation,
   (ii) phenotypes and diseases, (iii) data related to the environment and
   experimental conditions and (iv) datasets and software tools that allow
   the user to explore and analyze the interactions among these and their
   impact on disease.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Shimoyama, M (Corresponding Author), Med Coll Wisconsin, Human \& Mol Genet Ctr, Milwaukee, WI 53226 USA.
   Shimoyama, Mary; De Pons, Jeff; Hayman, G. Thomas; Laulederkind, Stanley J. F.; Liu, Weisong; Nigam, Rajni; Petri, Victoria; Smith, Jennifer R.; Tutaj, Marek; Wang, Shur-Jen; Worthey, Elizabeth; Dwinell, Melinda; Jacob, Howard, Med Coll Wisconsin, Human \& Mol Genet Ctr, Milwaukee, WI 53226 USA.
   Shimoyama, Mary, Med Coll Wisconsin, Dept Surg, Milwaukee, WI 53226 USA.
   Worthey, Elizabeth, Med Coll Wisconsin, Dept Pediat, Milwaukee, WI 53226 USA.
   Dwinell, Melinda; Jacob, Howard, Med Coll Wisconsin, Dept Physiol, Milwaukee, WI 53226 USA.},
DOI = {10.1093/nar/gku1026},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {CONTROLLED VOCABULARY; ONTOLOGY; ANNOTATION; RGD},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {shimoyama@mcw.edu},
Affiliations = {Medical College of Wisconsin; Medical College of Wisconsin; Medical
   College of Wisconsin; Medical College of Wisconsin},
ResearcherID-Numbers = {Laulederkind, Stanley/GLQ-8970-2022},
Funding-Acknowledgement = {National Heart, Lung, and Blood Institute on behalf of the National
   Institutes of Health {[}HL64541]; National Institutes of Health},
Funding-Text = {Support for this project was provided by the National Heart, Lung, and
   Blood Institute on behalf of the National Institutes of Health
   {[}HL64541]. Funding for open access charge: National Institutes of
   Health.},
Number-of-Cited-References = {29},
Times-Cited = {168},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {CC2YF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000350210400108},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000284148900012,
Author = {Du, Zhou and Zhou, Xin and Ling, Yi and Zhang, Zhenhai and Su, Zhen},
Title = {agriGO: a GO analysis toolkit for the agricultural community},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2010},
Volume = {38},
Number = {2},
Pages = {W64-W70},
Month = {JUL},
Abstract = {Gene Ontology (GO), the de facto standard in gene functionality
   description, is used widely in functional annotation and enrichment
   analysis. Here, we introduce agriGO, an integrated web-based GO analysis
   toolkit for the agricultural community, using the advantages of our
   previous GO enrichment tool (EasyGO), to meet analysis demands from new
   technologies and research objectives. EasyGO is valuable for its
   proficiency, and has proved useful in uncovering biological knowledge in
   massive data sets from high-throughput experiments. For agriGO, the
   system architecture and website interface were redesigned to improve
   performance and accessibility. The supported organisms and gene
   identifiers were substantially expanded (including 38 agricultural
   species composed of 274 data types). The requirement on user input is
   more flexible, in that user-defined reference and annotation are
   accepted. Moreover, a new analysis approach using Gene Set Enrichment
   Analysis strategy and customizable features is provided. Four tools, SEA
   (Singular enrichment analysis), PAGE (Parametric Analysis of Gene set
   Enrichment), BLAST4ID (Transfer IDs by BLAST) and SEACOMPARE (Cross
   comparison of SEA), are integrated as a toolkit to meet different
   demands. We also provide a cross-comparison service so that different
   data sets can be compared and explored in a visualized way. Lastly,
   agriGO functions as a GO data repository with search and download
   functions; agriGO is publicly accessible at
   http://bioinfo.cau.edu.cn/agriGO/.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Su, Z (Corresponding Author), China Agr Univ, Coll Biol Sci, State Key Lab Plant Physiol \& Biochem, Beijing 100193, Peoples R China.
   Du, Zhou; Zhou, Xin; Ling, Yi; Zhang, Zhenhai; Su, Zhen, China Agr Univ, Coll Biol Sci, State Key Lab Plant Physiol \& Biochem, Beijing 100193, Peoples R China.},
DOI = {10.1093/nar/gkq310},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {FALSE DISCOVERY RATE; GENE ONTOLOGY; ANNOTATION RESOURCE; DATABASE; SET;
   ENRICHMENT; BLAST2GO; RICE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {zhensu@cau.edu.cn},
Affiliations = {China Agricultural University},
ResearcherID-Numbers = {, 叮当๑/AAZ-9709-2020
   du, zhou/E-5358-2011},
Funding-Acknowledgement = {Ministry of Science and Technology of China {[}90817006, 2006CB100105]},
Funding-Text = {Funding for open access: Ministry of Science and Technology of China
   (90817006 and 2006CB100105).},
Number-of-Cited-References = {33},
Times-Cited = {1957},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {51},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {679GD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000284148900012},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000396575500118,
Author = {Viennas, Emmanouil and Komianou, Angeliki and Mizzi, Clint and
   Stojiljkovic, Maja and Mitropoulou, Christina and Muilu, Juha and
   Vihinen, Mauno and Grypioti, Panagiota and Papadaki, Styliani and
   Pavlidis, Cristiana and Zukic, Branka and Katsila, Theodora and van der
   Spek, Peter J. and Pavlovic, Sonja and Tzimas, Giannis and Patrinos,
   George P.},
Title = {Expanded national database collection and data coverage in the FINDbase
   worldwide database for clinically relevant genomic variation allele
   frequencies},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2017},
Volume = {45},
Number = {D1},
Pages = {D846-D853},
Month = {JAN 4},
Abstract = {FINDbase (http://www.findbase.org) is a comprehensive data repository
   that records the prevalence of clinically relevant genomic variants in
   various populations worldwide, such as pathogenic variants leadingmostly
   tomonogenic disorders and pharmacogenomics biomarkers. The database also
   records the incidence of rare genetic diseases in various populations,
   all in well-distinct data modules. Here, we report extensive data
   content updates in all data modules, with direct implications to
   clinical pharmacogenomics. Also, we report significant new developments
   in FINDbase, namely (i) the release of a new version of the ETHNOS
   software that catalyzes development curation of national/ethnic genetic
   databases, (ii) the migration of all FINDbase data content into 90
   distinct national/ethnicmutation databases, all built around Microsoft's
   PivotViewer (http://www.getpivot.com) software (iii) new data
   visualization tools and (iv) the interrelation of FINDbase with DruGeVar
   database with direct implications in clinical pharmacogenomics. The
   abovementioned updates further enhance the impact of FIND-base, as a key
   resource for Genomic Medicine applications.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Patrinos, GP (Corresponding Author), Univ Patras, Sch Hlth Sci, Dept Pharm, GR-26504 Patras, Greece.
   Patrinos, GP (Corresponding Author), Erasmus Univ, Med Ctr, Fac Med \& Hlth Sci, Dept Bioinformat, NL-3015 CN Rotterdam, Netherlands.
   Viennas, Emmanouil, Univ Patras, Fac Engn, Dept Comp Engn \& Informat, GR-26504 Patras, Greece.
   Komianou, Angeliki; Grypioti, Panagiota; Papadaki, Styliani; Pavlidis, Cristiana; Katsila, Theodora; Patrinos, George P., Univ Patras, Sch Hlth Sci, Dept Pharm, GR-26504 Patras, Greece.
   Mizzi, Clint; van der Spek, Peter J.; Patrinos, George P., Erasmus Univ, Med Ctr, Fac Med \& Hlth Sci, Dept Bioinformat, NL-3015 CN Rotterdam, Netherlands.
   Mizzi, Clint; Zukic, Branka; Pavlovic, Sonja, Univ Malta, Fac Med \& Surg, Dept Physiol \& Biochem, Msida 2090, Malta.
   Stojiljkovic, Maja, Univ Belgrade, Inst Mol Genet \& Genet Engn, Lab Mol Biomed, Belgrade 11010, Serbia.
   Mitropoulou, Christina, Golden Helix Fdn, London WC2N 5AP, England.
   Muilu, Juha, Univ Helsinki, Inst Mol Med Finland FIMM, FI-00014 Helsinki, Finland.
   Vihinen, Mauno, Lund Univ, Dept Expt Med Sci, SE-22100 Lund, Sweden.
   Tzimas, Giannis, Technol Educ Inst Western Greece, Dept Comp \& Informat Engn, GR-30020 Patras, Greece.
   Muilu, Juha, BC Platforms, Espoo, Finland.},
DOI = {10.1093/nar/gkw949},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PHARMACOGENOMICS; MICROATTRIBUTION; DOMAIN; DRUGS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {gpatrinos@upatras.gr},
Affiliations = {University of Patras; University of Patras; Erasmus University
   Rotterdam; Erasmus MC; University of Malta; University of Belgrade;
   University of Helsinki; Lund University; Western Greece University of
   Applied Sciences (TEI of Western Greece)},
ResearcherID-Numbers = {Mitropoulou, Christina/C-2851-2009
   Muilu, Juha/H-2474-2014
   van der Horst, Gijsbertus (Bert)/E-3661-2015
   Vihinen, Mauno/A-8452-2012
   Katsila, Theodora/O-3228-2015
   Tzimas, Giannis/R-5550-2019
   },
ORCID-Numbers = {Muilu, Juha/0000-0002-1034-5171
   van der Horst, Gijsbertus (Bert)/0000-0002-7773-6396
   Vihinen, Mauno/0000-0002-9614-7976
   Katsila, Theodora/0000-0002-6263-4231
   Tzimas, Giannis/0000-0002-4073-7256
   van der Spek, Peter/0000-0002-2203-0652},
Funding-Acknowledgement = {European Commission {[}FP7-200754, FP7-305444, FP7-285950, H2020-668353,
   FP7-316088]; Greek State grant; Serbian State grant {[}MESTD] {[}III
   41004]; Golden Helix Foundation (UK)},
Funding-Text = {European Commission {[}GEN2PHEN (FP7-200754), RD-CONNECT (FP7-305444),
   SEE DRUG (FP7-285950), UPGx (H2020-668353) to G.P.P. and SERBORDISInn
   (FP7-316088) to S.P.]; Greek State grant {[}E Pi AvEK 2014-2020; ELIXIR
   GR) to G.P.P.]; Serbian State grant {[}III 41004 MESTD RS to S.P.];
   Golden Helix Foundation (UK). Funding for open access charge: European
   Commission UPGx grant {[}H2020-668353].},
Number-of-Cited-References = {19},
Times-Cited = {13},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {EO3DQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000396575500118},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000608437800185,
Author = {Berrios, Daniel C. and Galazka, Jonathan and Grigorev, Kirill and Gebre,
   Samrawit and Costes, V, Sylvain},
Title = {NASA GeneLab: interfaces for the exploration of space omics data},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2021},
Volume = {49},
Number = {D1},
Pages = {D1515-D1522},
Month = {JAN 8},
Abstract = {The mission of NASA's GeneLab database (https: //genelab.nasa.gov/) is
   to collect, curate, and provide access to the genomic, transcriptomic,
   proteomic and metabolomic (so-called `omics') data from biospecimens
   flown in space or exposed to simulated space stressors, maximizing their
   utilization. This large collection of data enables the exploration of
   molecular network responses to space environments using a systems
   biology approach. We review here the various components of the GeneLab
   platform, including the new data repository web interface, and the
   GeneLab Online Data Entry (GEODE) web portal, which will support the
   expansion of the database in the future to include companion nonomics
   assay data. We discuss our design for GEODE, particularly how it
   promotes investigators providing more accurate metadata, reducing the
   curation effort required of GeneLab staff. We also introduce here a new
   GeneLab Application Programming Interface (API) specifically designed to
   support tools for the visualization of processed omics data. We review
   the outreach efforts by GeneLab to utilize the spaceflight data in the
   repository to generate novel discoveries and develop new hypotheses,
   including spearheading data analysis working groups, and a high school
   student training program. All these efforts are aimed ultimately at
   supporting precision risk management for human space exploration.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Costes, SV (Corresponding Author), NASA, Ames Res Ctr, Moffett Field, CA 94035 USA.
   Berrios, Daniel C., USRA NASA Ames Res Ctr, Moffett Field, CA 94035 USA.
   Galazka, Jonathan; Costes, Sylvain, V, NASA, Ames Res Ctr, Moffett Field, CA 94035 USA.
   Grigorev, Kirill, Weill Cornell Med, New York, NY 10065 USA.
   Gebre, Samrawit, KBR NASA Ames Res Ctr, Moffett Field, CA 94035 USA.},
DOI = {10.1093/nar/gkaa887},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {LOW-LET RADIATION; RISK},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {sylvain.v.costes@nasa.gov},
Affiliations = {National Aeronautics \& Space Administration (NASA); NASA Ames Research
   Center; Cornell University; Weill Cornell Medicine},
ORCID-Numbers = {Berrios, Daniel/0000-0003-4312-9552},
Funding-Acknowledgement = {Space Biology Program (Science Mission Directorate, Biological and
   Physical Sciences Division) of the National Aeronautics and Space
   Administration; NASA},
Funding-Text = {Space Biology Program (Science Mission Directorate, Biological and
   Physical Sciences Division) of the National Aeronautics and Space
   Administration. Funding for open access charge: NASA.},
Number-of-Cited-References = {30},
Times-Cited = {40},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {PT2GR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000608437800185},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000438374100074,
Author = {Kolbowski, Lars and Combe, Colin and Rappsilber, Juri},
Title = {xiSPEC: web-based visualization, analysis and sharing of proteomics data},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2018},
Volume = {46},
Number = {W1},
Pages = {W473-W478},
Month = {JUL 2},
Abstract = {We present xiSPEC, a standard compliant, next-generation web-based
   spectrum viewer for visualizing, analyzing and sharing mass spectrometry
   data. Peptide-spectrum matches from standard proteomics and
   cross-linking experiments are supported. xiSPEC is to date the only
   browser-based tool supporting the standardized file formats mzML and
   mzIdentML defined by the proteomics standards initiative. Users can
   either upload data directly or select files from the PRIDE data
   repository as input. xiSPEC allows users to save and share their
   datasets publicly or password protected for providing access to
   collaborators or readers and reviewers of manuscripts. The
   identification table features advanced interaction controls and spectra
   are presented in three interconnected views: (i) annotated mass
   spectrum, (ii) peptide sequence fragmentation key and (iii) quality
   control error plots of matched fragments. Highlighting or selecting data
   points in any view is represented in all other views. Views are
   interactive scalable vector graphic elements, which can be exported,
   e.g. for use in publication. xiSPEC allows for re-annotation of spectra
   for easy hypothesis testing by modifying input data. xiSPEC is freely
   accessible at http://spectrumviewer.org and the source code is openly
   available on https://github.com/Rappsilber-Laboratory/xiSPEC.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Rappsilber, J (Corresponding Author), Univ Edinburgh, Sch Biol Sci, Wellcome Ctr Cell Biol, Edinburgh EH9 3BF, Midlothian, Scotland.
   Rappsilber, J (Corresponding Author), Tech Univ Berlin, Inst Biotechnol, Bioanalyt, D-13355 Berlin, Germany.
   Kolbowski, Lars; Combe, Colin; Rappsilber, Juri, Univ Edinburgh, Sch Biol Sci, Wellcome Ctr Cell Biol, Edinburgh EH9 3BF, Midlothian, Scotland.
   Kolbowski, Lars; Rappsilber, Juri, Tech Univ Berlin, Inst Biotechnol, Bioanalyt, D-13355 Berlin, Germany.},
DOI = {10.1093/nar/gky353},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MASS-SPECTROMETRY; PROTEIN IDENTIFICATION; PRIDE; PLATFORM; PEPTIDE;
   VIEWER},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {juri.rappsilber@tu-berlin.de},
Affiliations = {University of Edinburgh; Technical University of Berlin},
ResearcherID-Numbers = {Rappsilber, Juri/B-7265-2015
   Rappsilber, Juri/ABF-3328-2020
   },
ORCID-Numbers = {Rappsilber, Juri/0000-0001-5999-1310
   Combe, Colin William/0000-0003-2526-2587
   Kolbowski, Lars Bernhard/0000-0001-6819-6570},
Funding-Acknowledgement = {Einstein Foundation; Wellcome Trust Senior Research Fellowship
   {[}103139]; Wellcome Trust Multi-user Equipment Grant {[}108504];
   Wellcome Centre for Cell Biology {[}203149]},
Funding-Text = {Einstein Foundation; Wellcome Trust Senior Research Fellowship {[}103139
   to J.R.]; Wellcome Trust Multi-user Equipment Grant {[}108504]; Wellcome
   Centre for Cell Biology {[}203149]. Funding for open access charge:
   Wellcome Centre for Cell Biology {[}203149].},
Number-of-Cited-References = {28},
Times-Cited = {26},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {GM7NC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000438374100074},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000490556600004,
Author = {Mehtonen, Juha and Polonen, Petri and Hayrynen, Sergei and Dufva, Olli
   and Lin, Jake and Liuksiala, Thomas and Granberg, Kirsi and Lohi, Olli
   and Hautamaki, Ville and Nykter, Matti and Heinaniemi, Merja},
Title = {Data-driven characterization of molecular phenotypes across
   heterogeneous sample collections},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2019},
Volume = {47},
Number = {13},
Month = {JUL 26},
Abstract = {Existing large gene expression data repositories hold enormous potential
   to elucidate disease mechanisms, characterize changes in cellular
   pathways, and to stratify patients based on molecular profiles. To
   achieve this goal, integrative resources and tools are needed that allow
   comparison of results across datasets and data types. We propose an
   intuitive approach for data-driven stratifications of molecular profiles
   and benchmark our methodology using the dimensionality reduction
   algorithm t-distributed stochastic neighbor embedding (t-SNE) with
   multi-study and multi-platform data on hematological malignancies. Our
   approach enables assessing the contribution of biological versus
   technical variation to sample clustering, direct incorporation of
   additional datasets to the same low dimensional representation,
   comparison of molecular disease subtypes identified from separate t-SNE
   representations, and characterization of the obtained clusters based on
   pathway databases and additional data. In this manner, we performed an
   integrative analysis across multi-omics acute myeloid leukemia studies.
   Our approach indicated new molecular subtypes with differential survival
   and drug responsiveness among samples lacking fusion genes, including a
   novel myelodysplastic syndrome-like cluster and a cluster characterized
   with CEBPA mutations and differential activity of the
   S-adenosylmethionine-dependent DNA methylation pathway. In summary,
   integration across multiple studies can help to identify novel molecular
   disease subtypes and generate insight into disease biology.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Heinäniemi, M (Corresponding Author), Univ Eastern Finland, Sch Med, Inst Biomed, Kuopio, Finland.
   Nykter, M (Corresponding Author), Tampere Univ, Fac Med \& Hlth Technol, Tampere, Finland.
   Mehtonen, Juha; Polonen, Petri; Heinaniemi, Merja, Univ Eastern Finland, Sch Med, Inst Biomed, Kuopio, Finland.
   Hayrynen, Sergei; Lin, Jake; Liuksiala, Thomas; Granberg, Kirsi; Nykter, Matti, Tampere Univ, Fac Med \& Hlth Technol, Tampere, Finland.
   Dufva, Olli, Univ Helsinki, Hematol Res Unit Helsinki, Helsinki, Finland.
   Dufva, Olli, Helsinki Univ Hosp, Comprehens Canc Ctr, Dept Hematol, Helsinki, Finland.
   Liuksiala, Thomas; Lohi, Olli, Tampere Univ, Tampere Ctr Child Hlth Res, Tampere, Finland.
   Liuksiala, Thomas; Lohi, Olli, Tampere Univ Hosp, Tampere, Finland.
   Hautamaki, Ville, Univ Eastern Finland, Sch Comp, Joensuu, Finland.},
DOI = {10.1093/nar/gkz281},
Article-Number = {e76},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENE-EXPRESSION; CLASSIFICATION; LEUKEMIA},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {matti.nykter@tuni.fi
   merja.heinaniemi@uef.fi},
Affiliations = {University of Eastern Finland; Tampere University; University of
   Helsinki; University of Helsinki; Helsinki University Central Hospital;
   Tampere University; Tampere University; Tampere University Hospital;
   University of Eastern Finland},
ResearcherID-Numbers = {Heinaniemi, Merja/AAS-4530-2020
   Dufva, Olli/X-7225-2019
   Lohi, Olli/AAW-6157-2021
   },
ORCID-Numbers = {Heinaniemi, Merja/0000-0001-6190-3439
   Lohi, Olli/0000-0001-9195-0797
   Rautajoki, Kirsi Johanna/0000-0001-6549-7810
   Hautamaki, Ville/0000-0002-5885-0003
   Mehtonen, Juha/0000-0003-0554-4667
   Dufva, Olli/0000-0002-8084-0282
   Liuksiala, Thomas/0000-0003-1148-5405
   Nykter, Matti/0000-0001-6956-2843
   Lin, Jake/0000-0001-9928-1663},
Funding-Acknowledgement = {Academy of Finland {[}269474, 276634]; Finnish Cultural Foundation;
   Sigrid Juselius Foundation; Cancer Society of Finland; Nokia Foundation;
   University of Eastern Finland; Academy of Finland (AKA) {[}269474,
   276634] Funding Source: Academy of Finland (AKA)},
Funding-Text = {Academy of Finland {[}269474 to M.N., 276634 to M.H.]; The Finnish
   Cultural Foundation (Interdisciplinary Science Workshops to M.H.);
   Sigrid Juselius Foundation (to M.N.); Cancer Society of Finland (to
   M.N., M.H.); Nokia Foundation (to V.H.); University of Eastern Finland
   (to M.H.). Funding for open access charge: Cancer Society of Finland.},
Number-of-Cited-References = {44},
Times-Cited = {17},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {JE2WX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000490556600004},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:001007614500001,
Author = {Riedel, Pascal and von Schwerin, Reinhold and Schaudt, Daniel and
   Hafner, Alexander and Spaete, Christian},
Title = {ResNetFed: Federated Deep Learning Architecture for Privacy-Preserving
   Pneumonia Detection from COVID-19 Chest Radiographs},
Journal = {JOURNAL OF HEALTHCARE INFORMATICS RESEARCH},
Year = {2023},
Volume = {7},
Number = {2},
Pages = {203-224},
Month = {JUN},
Abstract = {Personal health data is subject to privacy regulations, making it
   challenging to apply centralized data-driven methods in healthcare,
   where personalized training data is frequently used. Federated Learning
   (FL) promises to provide a decentralized solution to this problem. In
   FL, siloed data is used for the model training to ensure data privacy.
   In this paper, we investigate the viability of the federated approach
   using the detection of COVID-19 pneumonia as a use case. 1411 individual
   chest radiographs, sourced from the public data repository COVIDx8 are
   used. The dataset contains radiographs of 753 normal lung findings and
   658 COVID-19 related pneumonias. We partition the data unevenly across
   five separate data silos in order to reflect a typical FL scenario. For
   the binary image classification analysis of these radiographs, we
   propose ResNetFed, a pre-trained ResNet50 model modified for federation
   so that it supports Differential Privacy. In addition, we provide a
   customized FL strategy for the model training with COVID-19 radiographs.
   The experimental results show that ResNetFed clearly outperforms locally
   trained ResNet50 models. Due to the uneven distribution of the data in
   the silos, we observe that the locally trained ResNet50 models perform
   significantly worse than ResNetFed models (mean accuracies of 63\% and
   82.82\%, respectively). In particular, ResNetFed shows excellent model
   performance in underpopulated data silos, achieving up to +34.9
   percentage points higher accuracy compared to local ResNet50 models.
   Thus, with ResNetFed, we provide a federated solution that can assist
   the initial COVID-19 screening in medical centers in a
   privacy-preserving manner.},
Publisher = {SPRINGERNATURE},
Address = {CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Riedel, P (Corresponding Author), Univ Appl Sci, Inst Informat, Prittwitzstr 10, D-89075 Ulm, Baden Wurttembe, Germany.
   Riedel, Pascal; von Schwerin, Reinhold; Schaudt, Daniel; Hafner, Alexander, Univ Appl Sci, Inst Informat, Prittwitzstr 10, D-89075 Ulm, Baden Wurttembe, Germany.
   Spaete, Christian, Transferzentrum Digitalisierung Analyt \& Data Sci, Ensingerstr 4, D-89073 Ulm, Baden Wurttembe, Germany.},
DOI = {10.1007/s41666-023-00132-7},
EarlyAccessDate = {JUN 2023},
ISSN = {2509-4971},
EISSN = {2509-498X},
Keywords = {Federated learning; Deep learning; ResNet; Medical imaging; COVID-19},
Research-Areas = {Computer Science; Health Care Sciences \& Services; Medical Informatics},
Web-of-Science-Categories  = {Computer Science, Information Systems; Health Care Sciences \& Services;
   Medical Informatics},
Author-Email = {pascal.riedel@thu.de
   reinhold.vonschwerin@thu.de
   daniel.schaudt@thu.de
   alexander.hafner@thu.de
   christian.spaete@dasu.digital},
ORCID-Numbers = {Schaudt, Daniel/0000-0002-7920-7586},
Funding-Acknowledgement = {Projekt DEAL},
Funding-Text = {Open Access funding enabled and organized by Projekt DEAL.},
Number-of-Cited-References = {60},
Times-Cited = {2},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Healthc. Inform. Res.},
Doc-Delivery-Number = {J8DN5},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001007614500001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000296096800001,
Author = {Gower, Adam C. and Spira, Avrum and Lenburg, Marc E.},
Title = {Discovering biological connections between experimental conditions based
   on common patterns of differential gene expression},
Journal = {BMC BIOINFORMATICS},
Year = {2011},
Volume = {12},
Month = {SEP 27},
Abstract = {Background: Identifying similarities between patterns of differential
   gene expression provides an opportunity to identify similarities between
   the experimental and biological conditions that give rise to these gene
   expression alterations. The growing volume of gene expression data in
   open data repositories such as the NCBI Gene Expression Omnibus (GEO)
   presents an opportunity to identify these gene expression similarities
   on a large scale across a diverse collection of datasets. We have
   developed a fast, pattern-based computational approach, named openSESAME
   (Search of Expression Signatures Across Many Experiments), that
   identifies datasets enriched in samples that display coordinate
   differential expression of a query signature. Importantly, openSESAME
   performs this search without prior knowledge of the phenotypic or
   experimental groups in the datasets being searched. This allows
   openSESAME to identify perturbations of gene expression that are due to
   phenotypic attributes that may not have been described in the sample
   annotation included in the repository.: To demonstrate the utility of
   openSESAME, we used gene expression signatures of two biological
   perturbations to query a set of 75,164 human expression profiles that
   were generated using Affymetrix microarrays and deposited in GEO. The
   first query, using a signature of estradiol treatment, identified
   experiments in which estrogen signaling was perturbed and also
   identified differences in estrogen signaling between estrogen
   receptor-positive and -negative breast cancers. The second query, which
   used a signature of silencing of the transcription factor p63 (a key
   regulator of epidermal differentiation), identified datasets related to
   stratified squamous epithelia or epidermal diseases such as melanoma.
   Conclusions: openSESAME is a tool for leveraging the growing body of
   publicly available microarray data to discover relationships between
   different biological states based on common patterns of differential
   gene expression. These relationships may serve to generate hypotheses
   about the causes and consequences of specific patterns of observed
   differential gene expression. To encourage others to explore the utility
   of this approach, we have made a website for performing openSESAME
   queries freely available at http://opensesame.bu.edu.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Lenburg, ME (Corresponding Author), Boston Univ, Bioinformat Program, 44 Cummington St, Boston, MA 02215 USA.
   Gower, Adam C.; Spira, Avrum; Lenburg, Marc E., Boston Univ, Bioinformat Program, Boston, MA 02215 USA.
   Spira, Avrum; Lenburg, Marc E., Boston Univ, Sch Med, Dept Med, Div Computat Biomed, Boston, MA 02118 USA.},
DOI = {10.1186/1471-2105-12-381},
Article-Number = {381},
ISSN = {1471-2105},
Keywords-Plus = {HUMAN BREAST-CANCER; CELL-LINES; SIGNATURE; P63; P53; PROLIFERATION;
   CLASSIFICATION; INHIBITOR; RESISTANT; CARCINOMA},
Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
   Microbiology; Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
   Mathematical \& Computational Biology},
Author-Email = {mlenburg@bu.edu},
Affiliations = {Boston University; Boston University},
ResearcherID-Numbers = {Lenburg, Marc E/B-8027-2008
   },
ORCID-Numbers = {Lenburg, Marc E/0000-0002-5760-4708
   Spira, Avrum/0000-0003-1467-0489
   Gower, Adam/0000-0002-6122-7511},
Funding-Acknowledgement = {NCI {[}R01 CA124640, UL1 RR025771]; Ruth L. Kirschstein National
   Research Service {[}5 T32 HL07035]},
Funding-Text = {Supported by grants NCI R01 CA124640 and UL1 RR025771 to A.S. and M.E.
   L. and a Ruth L. Kirschstein National Research Service Award (\#5 T32
   HL07035) to A.C.G. We thank D. Center and R. Friedman of the Boston
   University Clinical and Translational Research Institute, C. Berg, B.
   Bassey and A. Rossi of the Medical Information Systems Unit of Boston
   Medical Center, and D. Ulrich for development of the openSESAME web
   server, and A. Broka for help in procuring, storing and processing GEO
   data.},
Number-of-Cited-References = {63},
Times-Cited = {15},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {BMC Bioinformatics},
Doc-Delivery-Number = {836FV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000296096800001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000267889100103,
Author = {Seelow, Dominik and Schuelke, Markus and Hildebrandt, Friedhelm and
   Nuernberg, Peter},
Title = {HomozygosityMapper-an interactive approach to homozygosity mapping},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2009},
Volume = {37},
Pages = {W593-W599},
Month = {JUL 1},
Abstract = {Homozygosity mapping is a common method for mapping recessive traits in
   consanguineous families. In most studies, applications for multipoint
   linkage analyses are applied to determine the genomic region linked to
   the disease. Unfortunately, these are neither suited for very large
   families nor for the inclusion of tens of thousands of SNPs. Even if
   less than 10 000 markers are employed, such an analysis may easily last
   hours if not days. Here we present a web-based approach to homozygosity
   mapping. Our application stores marker data in a database into which
   users can directly upload their own SNP genotype files. Within a few
   minutes, the database analyses the data, detects homozygous stretches
   and provides an intuitive graphical interface to the results. The
   homozygosity in affected individuals is visualized genome-wide with the
   ability to zoom into single chromosomes and user-defined chromosomal
   regions. The software also displays the underlying genotypes in all
   samples. It is integrated with our candidate gene search engine,
   GeneDistiller, so that users can interactively determine the most
   promising gene. They can at any point restrict access to their data or
   make it public, allowing HomozygosityMapper to be used as a data
   repository for homozygosity-mapping studies. HomozygosityMapper is
   available at http://www.homozygositymapper.org/.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Seelow, D (Corresponding Author), Charite Univ Med Berlin, Dept Neuropaediat, Augustenburger Pl 1, D-13353 Berlin, Germany.
   Seelow, Dominik; Schuelke, Markus, Charite Univ Med Berlin, Dept Neuropaediat, D-13353 Berlin, Germany.
   Seelow, Dominik; Schuelke, Markus, Charite Univ Med Berlin, Neurocure Clin Res Ctr, D-13353 Berlin, Germany.
   Seelow, Dominik; Nuernberg, Peter, Univ Cologne, CCG, D-50674 Cologne, Germany.
   Seelow, Dominik; Nuernberg, Peter, Univ Cologne, Inst Genet, D-50674 Cologne, Germany.
   Hildebrandt, Friedhelm, Univ Michigan, Dept Pediat, Ann Arbor, MI 48109 USA.
   Nuernberg, Peter, Univ Cologne, CMMC, D-50931 Cologne, Germany.},
DOI = {10.1093/nar/gkp369},
ISSN = {0305-1048},
Keywords-Plus = {RECESSIVE TRAITS; LINKAGE ANALYSIS; INBREEDING COEFFICIENT; MUTATIONS;
   GENE; FAMILIES; LOCUS; IDENTIFICATION; ASSOCIATION; POPULATION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {dominik.seelow@charite.de},
Affiliations = {Free University of Berlin; Humboldt University of Berlin; Charite
   Universitatsmedizin Berlin; Free University of Berlin; Humboldt
   University of Berlin; Charite Universitatsmedizin Berlin; University of
   Cologne; University of Cologne; University of Michigan System;
   University of Michigan; University of Cologne},
ResearcherID-Numbers = {Seelow, Dominik/HGB-3124-2022
   },
ORCID-Numbers = {Seelow, Dominik/0000-0002-9746-4412
   Schuelke, Markus/0000-0003-2824-3891},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft {[}SFB 665 TP A6]},
Funding-Text = {Deutsche Forschungsgemeinschaft within the SFB 665 TP A6 `Developmental
   Disorders of the Nervous System'; NeuroCure Cluster of Excellence {[}Exc
   257] at the Charite, Berlin. Funding for open access charge: Charite
   LOM.},
Number-of-Cited-References = {38},
Times-Cited = {304},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {469IG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000267889100103},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000729784800001,
Author = {Le Guillarme, Nicolas and Thuiller, Wilfried},
Title = {TaxoNERD: Deep neural models for the recognition of taxonomic entities
   in the ecological and evolutionary literature},
Journal = {METHODS IN ECOLOGY AND EVOLUTION},
Year = {2022},
Volume = {13},
Number = {3},
Pages = {625-641},
Month = {MAR},
Abstract = {Easy access to multi-taxa information (e.g. distribution, traits, diet)
   in the scientific literature is essential to understand, map and predict
   all-inclusive biodiversity. Tools are needed to automatically extract
   useful information from the ever-growing corpus of ecological texts and
   feed this information to open data repositories. A prerequisite is the
   ability to recognise mentions of taxa in text, a special case of named
   entity recognition (NER). In recent years, deep learning-based NER
   systems have become ubiquitous, yielding state-of-the-art results in the
   general and biomedical domains. However, no such tool is available to
   ecologists wishing to extract information from the biodiversity
   literature. We propose a new tool called TaxoNERD that provides deep
   neural network (DNN) models to recognise taxon mentions in ecological
   documents. To achieve high performance, these models usually need to be
   trained on a large corpus of manually annotated text. Creating such a
   corpus is a laborious and costly process, with the result that manually
   annotated corpora in the ecological domain tend to be too small to learn
   an accurate DNN model from scratch. To address this issue, we leverage
   existing models pretrained on large biomedical corpora using transfer
   learning. The performance of our models is evaluated on four corpora and
   compared to the most popular taxonomic entity recognition tools. Our
   experiments suggest that existing taxonomic NER tools are not suited to
   the extraction of ecological information from text as they performed
   poorly on ecologically oriented corpora, either because they do not take
   account of the variability of taxon naming practices or because they do
   not generalise well to the ecological domain. Conversely, a
   domain-specific DNN-based tool like TaxoNERD outperformed the other
   approaches on an ecological information extraction task. Efforts are
   needed to raise ecological information extraction to the same level of
   performance as its biomedical counterpart. One promising direction is to
   leverage the huge corpus of unlabelled ecological texts to learn a
   language representation model that could benefit downstream tasks. These
   efforts could be highly beneficial to ecologists on the long term.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Le Guillarme, N (Corresponding Author), Univ Savoie Mt Blanc, Univ Grenoble Alpes, CNRS, LECA,Lab Ecol Alpine, Grenoble, France.
   Le Guillarme, Nicolas; Thuiller, Wilfried, Univ Savoie Mt Blanc, Univ Grenoble Alpes, CNRS, LECA,Lab Ecol Alpine, Grenoble, France.},
DOI = {10.1111/2041-210X.13778},
EarlyAccessDate = {DEC 2021},
ISSN = {2041-210X},
EISSN = {2041-2096},
Keywords = {biodiversity databases; deep learning; ecological information
   extraction; taxonomic entity recognition; transfer learning},
Keywords-Plus = {BIG-DATA},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {nicolas.leguillarme@univ-grenoble-alpes.fr},
Affiliations = {Communaute Universite Grenoble Alpes; Universite Grenoble Alpes (UGA);
   Centre National de la Recherche Scientifique (CNRS); Universite Savoie
   Mont Blanc},
ResearcherID-Numbers = {Thuiller, Wilfried/G-3283-2010
   },
ORCID-Numbers = {Thuiller, Wilfried/0000-0002-5388-5274
   Le Guillarme, Nicolas/0000-0003-4559-7579},
Funding-Acknowledgement = {Agence Nationale de la Recherche {[}ANR--16-CE02-0009, ANR-19-P3IA-0003]},
Funding-Text = {Agence Nationale de la Recherche, Grant/Award Number: ANR--16-CE02-0009
   and ANR-19-P3IA-0003},
Number-of-Cited-References = {59},
Times-Cited = {11},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Methods Ecol. Evol.},
Doc-Delivery-Number = {ZK8OI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000729784800001},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000598231600037,
Author = {Goodall, Richard and Armstrong, Alexander and Hughes, William and Fries,
   Charles A. and Marshall, Dominic and Harbinson, Eleanor B. and
   Salciccioli, Justin and Shalhoub, Joseph},
Title = {Trends in Decubitus Ulcer Disease Burden in European Union 15+
   Countries, from 1990 to 2017},
Journal = {PLASTIC AND RECONSTRUCTIVE SURGERY-GLOBAL OPEN},
Year = {2020},
Volume = {8},
Number = {11},
Month = {NOV},
Abstract = {Background: Decubitus ulcers (DU) are a common pathology with
   significant morbidity and financial implications for health services
   globally. This study aimed to compare the burden of DU across European
   Union (EU) 15+ countries between 1990 and 2017.
   Methods: Age-standardized incidence, mortality, and disability-adjusted
   life-years (DALYs) rates per 100,000 were extracted from the Global
   Burden of Disease Study online data repository for EU15+ countries (a
   group of 19 countries with comparable health expenditure, including the
   United States, Canada, the United Kingdom, and Australia). A joinpoint
   regression analysis was used to describe trends.
   Results: The incidence of DU increased between 1990 and 2017 in 15 of 19
   EU15+ countries for both men and women. Mortality from DU decreased over
   the time period analyzed in the majority of EU15+ countries: only in
   Denmark, Finland, and Germany were increasing mortality rates observed.
   Decreasing DALY rates were generally observed, with the largest
   decreases observed in Ireland for men and women. Denmark and Germany
   were the only countries to demonstrate unfavorable trends in mortality,
   incidence, and DALYs between 1990 and 2017 for men and women. The United
   States, the Netherlands, and France were the only EU15+ countries in
   which improving disease burden was identified between 1990 and 2017 for
   all parameters assessed.
   Conclusions: Incidence of DU is increasing in EU15+ countries, whereas
   mortality rates and DALYs are improving. The trends in disease burden in
   Denmark and Germany have followed contrasting and unfavorable trends.
   Investigation into these trends is called for.},
Publisher = {LIPPINCOTT WILLIAMS \& WILKINS},
Address = {TWO COMMERCE SQ, 2001 MARKET ST, PHILADELPHIA, PA 19103 USA},
Type = {Article},
Language = {English},
Affiliation = {Goodall, R (Corresponding Author), Imperial Coll London, Charing Cross Hosp, Dept Surg \& Canc, Acad Sect Vasc Surg, Fulham Palace Rd, London W6 8RF, England.
   Goodall, Richard; Marshall, Dominic, Imperial Coll London, London, England.
   Goodall, Richard; Armstrong, Alexander; Fries, Charles A., Oxford Univ Hosp NHS Fdn Trust, Dept Plast Surg, Oxford, England.
   Hughes, William, Broomfield Hosp, Dept Plast Surg, Broomfield, England.
   Harbinson, Eleanor B., Royal Berkshire Hosp, Reading, Berks, England.
   Salciccioli, Justin, Harvard Med Sch, Mt Auburn Hosp, Dept Med, Cambridge, MA USA.
   Shalhoub, Joseph, Imperial Coll Healthcare NHS Trust, Imperial Coll London, London, England.},
DOI = {10.1097/GOX.0000000000003252},
Article-Number = {e3252},
ISSN = {2169-7574},
Keywords-Plus = {PREVALENCE},
Research-Areas = {Surgery},
Web-of-Science-Categories  = {Surgery},
Author-Email = {r.goodall@imperial.ac.uk},
Affiliations = {Imperial College London; Oxford University Hospitals NHS Foundation
   Trust; Mid Essex Hospital Services NHS Trust; Broomfield Hospital; Royal
   Berkshire Hospital; Harvard University; Mount Auburn Hospital; Imperial
   College London},
ResearcherID-Numbers = {Shalhoub, Joseph/P-2171-2014
   },
ORCID-Numbers = {Shalhoub, Joseph/0000-0003-1011-7440
   Marshall, Dominic/0000-0002-3498-2511},
Funding-Acknowledgement = {Imperial College London},
Funding-Text = {The authors thank Imperial College London for supporting the open access
   fees.},
Number-of-Cited-References = {21},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {PRS-GLOB. OPEN},
Doc-Delivery-Number = {PE2XK},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000598231600037},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000298601300148,
Author = {Sui, Shannan J. Ho and Begley, Kimberly and Reilly, Dorothy and Chapman,
   Brad and McGovern, Ray and Rocca-Sera, Philippe and Maguire, Eamonn and
   Altschuler, Gabriel M. and Hansen, Terah A. A. and Sompallae,
   Ramakrishna and Krivtsov, Andrei and Shivdasani, Ramesh A. and
   Armstrong, Scott A. and Culhane, Aedin C. and Correll, Mick and Sansone,
   Susanna-Assunta and Hofmann, Oliver and Hide, Winston},
Title = {The Stem Cell Discovery Engine: an integrated repository and analysis
   system for cancer stem cell comparisons},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2012},
Volume = {40},
Number = {D1},
Pages = {D984-D991},
Month = {JAN},
Abstract = {Mounting evidence suggests that malignant tumors are initiated and
   maintained by a subpopulation of cancerous cells with biological
   properties similar to those of normal stem cells. However, descriptions
   of stem-like gene and pathway signatures in cancers are inconsistent
   across experimental systems. Driven by a need to improve our
   understanding of molecular processes that are common and unique across
   cancer stem cells (CSCs), we have developed the Stem Cell Discovery
   Engine (SCDE)-an online database of curated CSC experiments coupled to
   the Galaxy analytical framework. The SCDE allows users to consistently
   describe, share and compare CSC data at the gene and pathway level. Our
   initial focus has been on carefully curating tissue and cancer stem
   cell-related experiments from blood, intestine and brain to create a
   high quality resource containing 53 public studies and 1098 assays. The
   experimental information is captured and stored in the multi-omics
   Investigation/Study/Assay (ISA-Tab) format and can be queried in the
   data repository. A linked Galaxy framework provides a comprehensive,
   flexible environment populated with novel tools for gene list
   comparisons against molecular signatures in GeneSigDB and MSigDB,
   curated experiments in the SCDE and pathways in WikiPathways. The SCDE
   is available at http://discovery.hsci.harvard.edu.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Hide, W (Corresponding Author), Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA.
   Sui, Shannan J. Ho; Begley, Kimberly; Reilly, Dorothy; Chapman, Brad; McGovern, Ray; Altschuler, Gabriel M.; Hansen, Terah A. A.; Sompallae, Ramakrishna; Culhane, Aedin C.; Hofmann, Oliver; Hide, Winston, Harvard Univ, Sch Publ Hlth, Dept Biostat, Boston, MA 02115 USA.
   Sui, Shannan J. Ho; Begley, Kimberly; Reilly, Dorothy; Chapman, Brad; McGovern, Ray; Hansen, Terah A. A.; Hofmann, Oliver; Hide, Winston, Harvard Univ, Sch Publ Hlth, HSPH Bioinformat Core, Boston, MA 02115 USA.
   Reilly, Dorothy; Sansone, Susanna-Assunta, Novartis Inst BioMed Res, Cambridge, MA USA.
   Rocca-Sera, Philippe; Maguire, Eamonn, Univ Oxford, Oxford E Res Ctr, Oxford OX1 2JD, England.
   Krivtsov, Andrei; Armstrong, Scott A., Childrens Hosp, Dept Pediat Oncol, Boston, MA 02115 USA.
   Culhane, Aedin C.; Correll, Mick, Dana Farber Canc Inst, Dept Biostat, Boston, MA 02115 USA.
   Krivtsov, Andrei; Shivdasani, Ramesh A.; Armstrong, Scott A., Harvard Univ, Sch Med, Boston, MA 02115 USA.
   Shivdasani, Ramesh A.; Armstrong, Scott A.; Hide, Winston, Harvard Stem Cell Inst, Cambridge, MA USA.
   Correll, Mick, Dana Farber Canc Inst, Ctr Canc Computat Biol, Boston, MA 02115 USA.},
DOI = {10.1093/nar/gkr1051},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENE-EXPRESSION; SURVIVAL; ONTOLOGY; DATABASE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {shosui@hsph.harvard.edu
   whide@hsph.harvard.edu},
Affiliations = {Harvard University; Harvard T.H. Chan School of Public Health; Harvard
   University; Harvard T.H. Chan School of Public Health; Novartis;
   University of Oxford; Harvard University; Boston Children's Hospital;
   Harvard University; Dana-Farber Cancer Institute; Harvard University;
   Harvard Medical School; Harvard University; Harvard University;
   Dana-Farber Cancer Institute},
ResearcherID-Numbers = {Krivtsov, Andrei/AAJ-9966-2021
   Hide, Winston/HKO-8176-2023
   Sui, Shannan Janelle/HTL-6887-2023
   Hide, Winston Hide/C-7217-2009
   Culhane, Aedin C/AAG-8490-2019
   Hide, Winston/R-3815-2019
   Hide, Winston A/V-2727-2017
   Hofmann, Oliver M/F-1800-2013
   },
ORCID-Numbers = {Hide, Winston/0000-0002-8621-3271
   Sui, Shannan Janelle/0000-0002-6191-4709
   Hide, Winston Hide/0000-0002-8621-3271
   Culhane, Aedin C/0000-0002-1395-9734
   Hide, Winston/0000-0002-8621-3271
   Hide, Winston A/0000-0002-8621-3271
   Hofmann, Oliver M/0000-0002-7738-1513
   Reilly, Dorothy/0000-0002-6677-3132
   Sansone, Susanna-Assunta/0000-0001-5306-5690
   Maguire, Eamonn/0000-0002-7277-7834
   Chapman, Brad/0000-0002-3026-1856},
Funding-Acknowledgement = {National Institutes of Health {[}1RC2CA148222-01]; Harvard Stem Cell
   Institute; Harvard School of Public Health; BBSRC {[}BB/I025840/1,
   BB/I000771/1, BB/E025080/1] Funding Source: UKRI; Biotechnology and
   Biological Sciences Research Council {[}BB/I000771/1, BB/I025840/1,
   BB/E025080/1] Funding Source: researchfish},
Funding-Text = {National Institutes of Health (1RC2CA148222-01 to R.S., S.A. and W.H.);
   Harvard Stem Cell Institute. Funding for open access charge: Harvard
   School of Public Health Dean's Fund; National Institutes of Health
   Stimulus awards.},
Number-of-Cited-References = {25},
Times-Cited = {17},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {869MD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000298601300148},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000996015700001,
Author = {Kale, Aditya U. and Mills, Andrew and Guggenheim, Emily and Gee, David
   and Bodza, Samuel and Anumakonda, Aparna and Doal, Rima and Williams,
   Rowena and Gallier, Suzy and Lee, Wen Hwa and Galsworthy, Paul and
   Benning, Manjit and Fanning, Hilary and Keane, Pearse A. and Denniston,
   Alastair K. and Mollan, Susan P.},
Title = {A Datasheet for the INSIGHT Birmingham, Solihull, and Black Country
   Diabetic Retinopathy Screening Dataset},
Journal = {OPHTHALMOLOGY SCIENCE},
Year = {2023},
Volume = {3},
Number = {3},
Month = {SEP},
Abstract = {Purpose: Diabetic retinopathy (DR) is the most common microvascular
   complication associated with diabetes mellitus (DM), affecting
   approximately 40\% of this patient population. Early detection of DR is
   vital to ensure monitoring of disease progression and prompt sight
   saving treatments as required. This article de-scribes the data
   contained within the INSIGHT Birmingham, Solihull, and Black Country
   Diabetic Retinopathy Dataset.Design: Dataset descriptor for routinely
   collected eye screening data.Participants: All diabetic patients aged 12
   years and older, attending annual digital retinal photography-based
   screening within the Birmingham, Solihull, and Black Country Eye
   Screening Programme.Methods: The INSIGHT Health Data Research Hub for
   Eye Health is a National Health Service (NHS)eled ophthalmic bioresource
   that provides researchers with safe access to anonymized, routinely
   collected data from contributing NHS hospitals to advance research for
   patient benefit. This report describes the INSIGHT Birmingham, Solihull,
   and Black Country DR Screening Dataset, a dataset of anonymized images
   and linked screening data derived from the United Kingdom's largest
   regional DR screening program.Main Outcome Measures: This dataset
   consists of routinely collected data from the eye screening program. The
   data primarily include retinal photographs with the associated DR
   grading data. Additional data such as corresponding demographic details,
   information regarding patients' diabetic status, and visual acuity data
   are also available. Further details regarding available data points are
   available in the supplementary information, in addition to the INSIGHT
   webpage included below.Results: At the time point of this analysis
   (December 31, 2019), the dataset comprised 6 202161 images from 246180
   patients, with a dataset inception date of January 1, 2007. The dataset
   includes 1 360 547 grading ep-isodes between R0M0 and R3M1.Conclusions:
   This dataset descriptor article summarizes the content of the dataset,
   how it has been curated, and what its potential uses are. Data are
   available through a structured application process for research studies
   that support discovery, clinical evidence analyses, and innovation in
   artificial intelligence technologies for patient benefit. Further
   information regarding the data repository and contact details can be
   found at https://www.in-sight.hdrhub.org/.Financial Disclosure(s):
   Proprietary or commercial disclosure may be found after the references.
   Ophthalmology Science 2023;3:100293 (c) 2023 by the American Academy of
   Ophthalmology. This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Mollan, SP (Corresponding Author), Univ Hosp Birmingham NHS Fdn Trust, Ophthalmol Dept, Birmingham, England.
   Kale, Aditya U.; Denniston, Alastair K., Univ Birmingham, Inst Inflammat \& Ageing, Coll Med \& Dent Sci, Acad Unit Ophthalmol, Birmingham, England.
   Kale, Aditya U.; Denniston, Alastair K.; Mollan, Susan P., Univ Hosp Birmingham NHS Fdn Trust, Ophthalmol Dept, Birmingham, England.
   Mills, Andrew; Galsworthy, Paul, Univ Hosp Birmingham NHS Fdn Trust, Birmingham Heartlands Hosp, Birmingham, England.
   Guggenheim, Emily; Gee, David; Bodza, Samuel; Anumakonda, Aparna; Doal, Rima; Williams, Rowena; Gallier, Suzy, Univ Hosp Birmingham NHS Fdn Trust, Hlth Informat, Birmingham, England.
   Lee, Wen Hwa; Benning, Manjit; Fanning, Hilary; Keane, Pearse A.; Denniston, Alastair K.; Mollan, Susan P., INSIGHT Hlth Data Res Hub Eye Hlth, Birmingham, England.
   Lee, Wen Hwa, Act Age Related Macular Degenerat, London, England.
   Benning, Manjit, Moor fields Eye Hosp NHS Fdn Trust, Moor fields Res \& Dev, London, England.
   Fanning, Hilary, Univ Hosp Birmingham NHS Fdn Trust, Res \& Dev, Birmingham, England.
   Keane, Pearse A., UCL Inst Ophthalmol, NIHR Biomed Res Ctr Moor fields Eye Hosp NHS Fdn T, London, England.},
DOI = {10.1016/j.xops.2023.100293},
EarlyAccessDate = {APR 2023},
Article-Number = {100293},
ISSN = {2666-9145},
Keywords = {Diabetic retinopathy; Biomedical data; Dataset; Diabetes mellitus;
   Imaging},
Keywords-Plus = {PREVALENCE; MANAGEMENT; HEALTH},
Research-Areas = {Ophthalmology},
Web-of-Science-Categories  = {Ophthalmology},
Author-Email = {soozmollan@doctors.org.uk},
Affiliations = {University of Birmingham; University of Birmingham; Heart of England NHS
   Foundation Trust; University of Birmingham; University of Birmingham;
   University of Birmingham; University of London; University College
   London},
Funding-Acknowledgement = {INSIGHT Hub; UK Research \& Innovation, via Medical Research Council and
   Health Data Research UK; Action Against Age-related Macular
   Degeneration-AAAMD; HDR UK and INSIGHT Hub grant; Grants-Moorfields Eye
   Charity Career Development Award; UK Research \& Innovation Future
   Leaders Fellowship; Health Data Research, United Kingdom (HDR UK);
   Medical Research Council (MRC); Engineering and Physical Sciences
   Research Council (EPSRC); Economic and Social Research Council (ESRC);
   National Institute for Health Research (NIHR); Chief Scientist Office of
   the Scottish Government Health and Social Care Directorates, Health and
   Social Care Research and Development Division (Welsh Government);
   Wellcome Trust Limited as trustee of the Wellcome Trust; British Heart
   Foundation (BHF); Velux Foundation; Payment or honoraria-Heidelberg
   Engineering; Well-come Trust Limited; Chugai-Roche Ltd; European
   Neuro-ophthalmology Society Research committee; United Kingdom
   Neuro-Ophthalmology Society committee and secretary {[}1170224,
   SC048549]; British Isles Neuro-Ophthalmology Club Trea-surer, Editorial
   Board of Neuro-Ophthalmology (Taylor Francis); Committee of the Journal
   of Neuro-Ophthalmology (Original contributions) {[}R190028A]; 
   {[}MR/T019050/1]},
Funding-Text = {All authors have completed and submitted the ICMJE disclosures form. The
   authors declare the following financial interests/personal relationships
   which may be considered as potential competing interests M.B.: Grant
   funding for the INSIGHT Hub awarded by UK Research \& Innovation, via
   Medical Research Council and Health Data Research UK. W.H.L.: Support
   from Action Against Age-related Macular Degeneration-AAAMD (Registered
   Charity numbers 1170224 {[}UK] and SC048549 {[}Scotland]), AAAMD is a
   Charity Partner in the INSIGHT Hub. Grants or contracts from HDR UK and
   INSIGHT Hub grant. Participation on a Data Safety Monitoring Board or
   Advisory Board from Data Trust Advisory Board (DataTAB) , DataTAB
   provides oversight and scrutiny to INSIGHT, by assessing individual
   applications to access data through INSIGHT. See https://
   www.insight.hdrhub.org/data-trust-advisory-board. Leadership or
   fiduciary role in other board CEO AAAMD. A.K.D.: Grant funding-Health
   Data Research, United Kingdom (HDR UK) October 2019-August 2022. P.A.K.:
   Grants-Moorfields Eye Charity Career Development Award R190028A
   (Institution) and UK Research \& Innovation Future Leaders Fellowship
   MR/T019050/1 (Institution) ; Consulting fees-Google, DeepMind, Roche,
   Noartis, Apellis, Bitfound. Payment or honoraria-Heidelberg Engineering,
   Topcon, Allergan, Bayer. H.F.: Grant funding for the INSIGHT Hub awarded
   by UK Research \& Innovation, via Medical Research Council and Health
   Data Research UK August 2019 to August 2022. INSIGHT is a National
   Health Service-led partnership established to improve healthcare by
   encouraging research using routinely collected eye data. INSIGHT is
   funded by Health Data Research, United Kingdom (HDR UK) . HDR UK is
   funded by the Medical Research Council (MRC) , Engineering and Physical
   Sciences Research Council (EPSRC) , Economic and Social Research Council
   (ESRC) , Na-tional Institute for Health Research (NIHR) ; Chief
   Scientist Office of the Scottish Government Health and Social Care
   Directorates, Health and So-cial Care Research and Development Division
   (Welsh Government; HCRW) , Public Health Agency (Northern Ireland; PHA)
   , British Heart Foundation (BHF) and the Wellcome Trust Limited as
   trustee of the Wellcome Trust. S.G.: Grants or contracts-HDRUK, MRC,
   NIHR. S.M.: Royalties or licenses-Springer publishing:
   Neuro-Ophthalmology and Global Trends in Diagnosis, Treatment and
   Management. Consulting fees-Invex therapeutics, Neurodiem, and Velux
   Foundation; Payment or honoraria-Heidelberg Engineering, Chugai-Roche
   Ltd, Allergan, Santen, Chiesi, Santhera. Leadership or fiduciary role in
   North American Neuro-ophthalmology society board, European
   Neuro-ophthalmology Society Research committee, United Kingdom
   Neuro-Ophthalmology Society committee and secretary, British Isles
   Neuro-Ophthalmology Club Trea-surer, Editorial Board of
   Neuro-Ophthalmology (Taylor \& Francis) , and Committee of the Journal
   of Neuro-Ophthalmology (Original contributions) .The other authors have
   no proprietary or commercial interest in any materials discussed in this
   article. INSIGHT is a National Health Service-led partnership
   established to improve health care by encouraging research using
   routinely collected eye data. INSIGHT is funded by Health Data Research,
   United Kingdom (HDR UK) .; HDR UK is funded by the Medical Research
   Council (MRC) , Engineering and Physical Sciences Research Council
   (EPSRC) , Economic and Social Research Council (ESRC) , National
   Institute for Health Research (NIHR) ; Chief Scientist Office of the
   Scottish Government Health and Social Care Directorates, Health and
   Social Care Research and Development Division (Welsh Government; HCRW) ,
   Public Health Agency (Northern Ireland; PHA) , British Heart Foundation
   (BHF) , and the Well-come Trust Limited as trustee of the Wellcome
   Trust.},
Number-of-Cited-References = {41},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Ophthalmol. Sci.},
Doc-Delivery-Number = {H4XS5},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000996015700001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000435176700087,
Author = {Baldi, Enrico and Contri, Enrico and Burkart, Roman and Borrelli, Paola
   and Ferraro, Ottavia Eleonora and Tonani, Michela and Cutuli, Amedeo and
   Bertaia, Daniele and Iozzo, Pasquale and Tinguely, Caroline and Lopez,
   Daniel and Boldarin, Susi and Deiuri, Claudio and Denereaz, Sandrine and
   Denereaz, Yves and Terrapon, Michael and Tami, Christian and Cereda,
   Cinzia and Somaschini, Alberto and Cornara, Stefano and Cortegiani,
   Andrea},
Title = {Protocol of a Multicenter International Randomized Controlled Manikin
   Study on Different Protocols of Cardiopulmonary Resuscitation for
   laypeople (MANI-CPR)},
Journal = {BMJ OPEN},
Year = {2018},
Volume = {8},
Number = {4},
Month = {APR},
Abstract = {Introduction Out-of-hospital cardiac arrest is one of the leading causes
   of death in industrialised countries. Survival depends on prompt
   identification of cardiac arrest and on the quality and timing of
   cardiopulmonary resuscitation (CPR) and defibrillation. For laypeople,
   there has been a growing interest on hands-only CPR, meaning continuous
   chest compression without interruption to perform ventilations. It has
   been demonstrated that intentional interruptions in hands-only CPR can
   increase its quality. The aim of this randomised trial is to compare
   three CPR protocols performed with different intentional interruptions
   with hands-only CPR.
   Methods and analysis This is a prospective randomised trial performed in
   eight training centres. Laypeople who passed a basic life support course
   will be randomised to one of the four CPR protocols in an 8 min
   simulated cardiac arrest scenario on a manikin: (1) 30 compressions and
   2 s pause; (2) 50 compressions and 5 s pause; (3) 100 compressions and
   10 s pause; (4) hands-only. The calculated sample size is 552 people.
   The primary outcome is the percentage of chest compression performed
   with correct depth evaluated by a computerised feedback system (Laerdal
   QCPR).
   Ethics and dissemination. Due to the nature of the study, we obtained a
   waiver from the Ethics Committee (IRCCS Policlinico San Matteo, Pavia,
   Italy). All participants will sign an informed consent form before
   randomisation. The results of this study will be published in
   peer-reviewed journal. The data collected will also be made available in
   a public data repository.},
Publisher = {BMJ PUBLISHING GROUP},
Address = {BRITISH MED ASSOC HOUSE, TAVISTOCK SQUARE, LONDON WC1H 9JR, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Baldi, E (Corresponding Author), Pavia Nel Cuore ONLUS, Pavia, Italy.
   Baldi, E (Corresponding Author), Robbio Nel Cuore ONLUS, Robbio, Italy.
   Baldi, E (Corresponding Author), Univ Pavia, Fdn IRCCS Policlin San Matteo, Sch Cardiovasc Dis, Pavia, Italy.
   Baldi, Enrico; Contri, Enrico; Tonani, Michela; Cutuli, Amedeo; Somaschini, Alberto; Cornara, Stefano, Pavia Nel Cuore ONLUS, Pavia, Italy.
   Baldi, Enrico; Contri, Enrico; Bertaia, Daniele, Robbio Nel Cuore ONLUS, Robbio, Italy.
   Baldi, Enrico; Somaschini, Alberto; Cornara, Stefano, Univ Pavia, Fdn IRCCS Policlin San Matteo, Sch Cardiovasc Dis, Pavia, Italy.
   Contri, Enrico, Fdn IRCCS Policlin San Matteo, Dept Anesthesia \& Intens Care, Pavia, Italy.
   Burkart, Roman, Swiss Resuscitat Council, Bern, Switzerland.
   Burkart, Roman, Fdn Ticino Cuore, Breganzona, Switzerland.
   Borrelli, Paola; Ferraro, Ottavia Eleonora, Univ Pavia, Dept Publ Hlth Expt \& Forens Med, Unit Biostat \& Clin Epidemiol, Pavia, Italy.
   Tonani, Michela, Osped Maggiore Lodi, Dept Emergency Med, Lodi, Italy.
   Iozzo, Pasquale, Univ Palermo, Gen Intens Care Unit, Policlin Paolo Giaccone, Palermo, Italy.
   Tinguely, Caroline; Lopez, Daniel, Emergency Training Ctr, Cugy, Switzerland.
   Boldarin, Susi; Deiuri, Claudio, Ctr Studi \& Formaz Gymnasium, Pordenone, Italy.
   Denereaz, Sandrine; Denereaz, Yves, ES ASUR, Lausanne, Switzerland.
   Terrapon, Michael, FormaMed Sarl, Cortaillod, Switzerland.
   Tami, Christian; Cereda, Cinzia, Federaz Cantonale Ticinese Serv Autoambulanze, Lugano, Switzerland.
   Tami, Christian; Cereda, Cinzia, AMUT, Breganzona, Switzerland.
   Cortegiani, Andrea, Univ Palermo, Policlin Paolo Giaccone, Sect Anesthesia Analgesia Intens Care \& Emergency, Dept Biopathol \& Med Biotechnol DIBIMED, Palermo, Italy.},
DOI = {10.1136/bmjopen-2017-019723},
Article-Number = {e019723},
ISSN = {2044-6055},
Keywords-Plus = {HOSPITAL CARDIAC-ARREST; AMERICAN-HEART-ASSOCIATION; COMPRESSION-ONLY
   CPR; BASIC LIFE-SUPPORT; CHEST COMPRESSION; VISUAL FEEDBACK; CARE
   COMMITTEE; SURVIVAL RATE; LAY-RESCUERS; STANDARD},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {enrico.baldi88@gmail.com},
Affiliations = {University of Pavia; IRCCS Fondazione San Matteo; IRCCS Fondazione San
   Matteo; University of Pavia; Ospedale Maggiore di Lodi; University of
   Palermo; Policlinico Paolo Giaccone; University of Palermo; Policlinico
   Paolo Giaccone},
ResearcherID-Numbers = {Ferraro, Ottavia Eleonora/V-2090-2019
   Baldi, Enrico/L-1245-2016
   Contri, Enrico/AAB-6797-2022
   Cortegiani, Andrea/H-4902-2016
   Borrelli, Paola/ABF-2045-2020
   },
ORCID-Numbers = {Ferraro, Ottavia Eleonora/0000-0002-4398-4885
   Baldi, Enrico/0000-0002-6360-224X
   Contri, Enrico/0000-0001-7507-0108
   Cortegiani, Andrea/0000-0003-1416-9993
   Borrelli, Paola/0000-0001-9389-627X
   Cornara, Stefano/0000-0002-4311-2139
   Somaschini, Alberto/0000-0003-1223-6128},
Funding-Acknowledgement = {Laerdal Italia},
Funding-Text = {Laerdal Italia provided funding to pay the open access publication
   charges for this article.},
Number-of-Cited-References = {29},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {BMJ Open},
Doc-Delivery-Number = {GJ3FT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000435176700087},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000886761700001,
Author = {Wu, Lianlian and Yan, Bowei and Han, Junshan and Li, Ruijiang and Xiao,
   Jian and He, Song and Bo, Xiaochen},
Title = {TOXRIC: a comprehensive database of toxicological data and benchmarks},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2023},
Volume = {51},
Number = {D1},
Pages = {D1432-D1445},
Month = {JAN 6},
Abstract = {The toxic effects of compounds on environment, humans, and other
   organisms have been a major focus of many research areas, including drug
   discovery and ecological research. Identifying the potential toxicity in
   the early stage of compound/drug discovery is critical. The rapid
   development of computational methods for evaluating various toxicity
   categories has increased the need for comprehensive and system-level
   collection of toxicological data, associated attributes, and benchmarks.
   To contribute toward this goal, we proposed TOXRIC (), a database with
   comprehensive toxicological data, standardized attribute data, practical
   benchmarks, informative visualization of molecular representations, and
   an intuitive function interface. The data stored in TOXRIC contains 113
   372 compounds, 13 toxicity categories, 1474 toxicity endpoints covering
   in vivo/in vitro endpoints and 39 feature types, covering structural,
   target, transcriptome, metabolic data, and other descriptors. All the
   curated datasets of endpoints and features can be retrieved, downloaded
   and directly used as output or input to Machine Learning (ML)-based
   prediction models. In addition to serving as a data repository, TOXRIC
   also provides visualization of benchmarks and molecular representations
   for all endpoint datasets. Based on these results, researchers can
   better understand and select optimal feature types, molecular
   representations, and baseline algorithms for each endpoint prediction
   task. We believe that the rich information on compound toxicology,
   ML-ready datasets, benchmarks and molecular representation distribution
   can greatly facilitate toxicological investigations, interpretation of
   toxicological mechanisms, compound/drug discovery and the development of
   computational methods.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {He, S; Bo, XC (Corresponding Author), Inst Hlth Serv \& Transfus Med, Dept Bioinformat, Beijing 100850, Peoples R China.
   Bo, XC (Corresponding Author), Tianjin Univ, Acad Med Engn \& Translat Med, Tianjin 300072, Peoples R China.
   Wu, Lianlian; Yan, Bowei; Han, Junshan; Li, Ruijiang; He, Song; Bo, Xiaochen, Inst Hlth Serv \& Transfus Med, Dept Bioinformat, Beijing 100850, Peoples R China.
   Wu, Lianlian; Bo, Xiaochen, Tianjin Univ, Acad Med Engn \& Translat Med, Tianjin 300072, Peoples R China.
   Yan, Bowei, Fudan Univ, Inst Biomed Sci, Human Phenome Inst,Sch Life Sci, State Key Lab Genet Engn \& Collaborat Innovat Ctr, Shanghai 200433, Peoples R China.
   Yan, Bowei, Beijing Proteome Res Ctr, Natl Ctr Prot Sci, State Key Lab Prote, Beijing 102206, Peoples R China.
   Xiao, Jian, Cent South Univ, Xiangya Hosp, Dept Pharm, Changsha 410008, Hunan, Peoples R China.
   Xiao, Jian, Cent South Univ, Xiangya Hosp, Inst Rat \& Safe Medicat Pract, Natl Clin Res Ctr forGeriatr Disorders, Changsha 410008, Hunan, Peoples R China.},
DOI = {10.1093/nar/gkac1074},
EarlyAccessDate = {NOV 2022},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {IN-VIVO EXTRAPOLATION; TOXCAST PROGRAM; DRUG DISCOVERY; TOXICITY; VITRO;
   RISK; EXPOSURE; TOXICOGENOMICS; ECOTOXICITY; DOSIMETRY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {hes1224@163.com
   boxc@bmi.ac.cn},
Affiliations = {Tianjin University; Fudan University; Central South University; Central
   South University},
ORCID-Numbers = {Bo, Xiao-chen/0000-0003-1911-7922
   Wu, Lianlian/0000-0002-9611-4488
   He, Song/0000-0002-4136-6151},
Funding-Acknowledgement = {National Natural Science Foundation of China {[}62103436]},
Funding-Text = {National Natural Science Foundation of China {[}62103436]. Funding for
   open access charge: National Natural Science Foundation of China
   {[}62103436].},
Number-of-Cited-References = {75},
Times-Cited = {7},
Usage-Count-Last-180-days = {13},
Usage-Count-Since-2013 = {25},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {Q5NY7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000886761700001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000419550700158,
Author = {Marzec, Jacek and Ullah, Abu Z. Dayem and Pirro, Stefano and Gadaleta,
   Emanuela and Crnogorac-Jurcevic, Tatjana and Lemoine, Nicholas R. and
   Kocher, Hemant M. and Chelala, Claude},
Title = {The Pancreatic Expression Database: 2018 update},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2018},
Volume = {46},
Number = {D1},
Pages = {D1107-D1110},
Month = {JAN 4},
Abstract = {The Pancreatic Expression Database (PED,
   http://www.pancreasexpression.org) continues to be a major resource for
   mining pancreatic -omics data a decade after its initial release. Here,
   we present recent updates to PED and describe its evolution into a
   comprehensive resource for extracting, analysing and integrating
   publicly available multiomics datasets. A new analytical module has been
   implemented to run in parallel with the existing literature mining
   functions. This analytical module has been created using rich data
   content derived from pancreas-related specimens available through the
   major data repositories (GEO, ArrayExpress) and international
   initiatives (TCGA, GENIE, CCLE). Researchers have access to a host of
   functions to tailor analyses to meet their needs. Results are presented
   using interactive graphics that allow the molecular data to be
   visualized in a user-friendly manner. Furthermore, researchers are
   provided with the means to superimpose layers of molecular information
   to gain greater insight into alterations and the relationships between
   them. The literature-mining module has been improved with a redesigned
   web appearance, restructured query platforms and updated annotations.
   These updates to PED are in preparation for its integration with the
   Pancreatic Cancer Research Fund Tissue Bank (PCRFTB), a vital resource
   of pancreas cancer tissue for researchers to support and promote
   cutting-edge research.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Chelala, C (Corresponding Author), Queen Mary Univ London, Barts Canc Inst, Ctr Mol Oncol, Bioinformat Unit, London EC1M 6BQ, England.
   Chelala, C (Corresponding Author), Queen Mary Univ London, Ctr Computat Biol, Life Sci Initiat, London, England.
   Marzec, Jacek; Ullah, Abu Z. Dayem; Pirro, Stefano; Gadaleta, Emanuela; Chelala, Claude, Queen Mary Univ London, Barts Canc Inst, Ctr Mol Oncol, Bioinformat Unit, London EC1M 6BQ, England.
   Crnogorac-Jurcevic, Tatjana; Lemoine, Nicholas R., Queen Mary Univ London, Barts Canc Inst, Ctr Mol Oncol, London EC1M 6BQ, England.
   Kocher, Hemant M., Queen Mary Univ London, Barts Canc Inst, Ctr Tumour Biol, London EC1M 6BQ, England.
   Chelala, Claude, Queen Mary Univ London, Ctr Computat Biol, Life Sci Initiat, London, England.},
DOI = {10.1093/nar/gkx955},
ISSN = {0305-1048},
EISSN = {1362-4962},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {c.chelala@qmul.ac.uk},
Affiliations = {University of London; Queen Mary University London; University of
   London; Queen Mary University London; University of London; Queen Mary
   University London; University of London; Queen Mary University London},
ResearcherID-Numbers = {Pirro, Stefano/AAA-9898-2019
   },
ORCID-Numbers = {Dayem Ullah, Abu/0000-0002-2567-4648
   Kocher, Hemant M/0000-0001-6771-1905
   Lemoine, Nick/0000-0001-8675-058X
   Pirro, Stefano/0000-0002-8601-722X
   chelala, claude/0000-0002-2488-0669},
Funding-Acknowledgement = {Pancreatic Cancer Research Fund {[}Tissue Bank grant]; Cancer Research
   UK {[}A12008]; Breast Cancer Campaign {[}Tissue Bank Bioinformatics
   grant] {[}TB2016BIF]; Cancer Research UK {[}12008] Funding Source:
   researchfish},
Funding-Text = {J.M. and A.Z.D.U. are funded by Pancreatic Cancer Research Fund
   {[}Tissue Bank grant, to H.K. and C.C.]; A.Z.D.U. was funded by Cancer
   Research UK {[}Grant A12008: to N.R.L., T.C.J. and C.C.]; S.P. and E.G.
   are funded by Breast Cancer Campaign {[}Tissue Bank Bioinformatics grant
   TB2016BIF to C.C.]. Funding for open access charge: Cancer Research UK
   {[}Grant A12008].},
Number-of-Cited-References = {21},
Times-Cited = {11},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {FS1QA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000419550700158},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000419550700167,
Author = {Cooper, Laurel and Meier, Austin and Laporte, Marie-Angelique and Elser,
   Justin L. and Mungall, Chris and Sinn, Brandon T. and Cavaliere, Dario
   and Carbon, Seth and Dunn, Nathan A. and Smith, Barry and Qu, Botong and
   Preece, Justin and Zhang, Eugene and Todorovic, Sinisa and Gkoutos,
   Georgios and Doonan, John H. and Stevenson, Dennis W. and Arnaud,
   Elizabeth and Jaiswal, Pankaj},
Title = {The Planteome database: an integrated resource for reference ontologies,
   plant genomics and phenomics},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2018},
Volume = {46},
Number = {D1},
Pages = {D1168-D1180},
Month = {JAN 4},
Abstract = {The Planteome project (http://www.planteome.org) provides a suite of
   reference and species-specific ontologies for plants and annotations to
   genes and phenotypes. Ontologies serve as common standards for semantic
   integration of a large and growing corpus of plant genomics, phenomics
   and genetics data. The reference ontologies include the Plant Ontology,
   Plant Trait Ontology and the Plant Experimental Conditions Ontology
   developed by the Planteome project, along with the Gene Ontology,
   Chemical Entities of Biological Interest, Phenotype and Attribute
   Ontology, and others. The project also provides access to
   species-specific Crop Ontologies developed by various plant breeding and
   research communities from around the world. We provide integrated data
   on plant traits, phenotypes, and gene function and expression from 95
   plant taxa, annotated with reference ontology terms. The Planteome
   project is developing a plant gene annotation platform; Planteome
   Noctua, to facilitate community engagement. All the Planteome ontologies
   are publicly available and are maintained at the Planteome GitHub site
   (https://github.com/Planteome) for sharing, tracking revisions and new
   requests. The annotated data are freely accessible from the ontology
   browser (http:browser//planteome.org/amigo) and our data repository.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Jaiswal, P (Corresponding Author), Oregon State Univ, Dept Bot \& Plant Pathol, Corvallis, OR 97331 USA.
   Cooper, Laurel; Meier, Austin; Elser, Justin L.; Preece, Justin; Jaiswal, Pankaj, Oregon State Univ, Dept Bot \& Plant Pathol, Corvallis, OR 97331 USA.
   Laporte, Marie-Angelique; Arnaud, Elizabeth, Biovers Int, Parc Sci Agropolis 2, F-34397 Montpellier 5, France.
   Mungall, Chris; Carbon, Seth; Dunn, Nathan A., Lawrence Berkeley Natl Lab, Environm Genom \& Syst Biol, Berkeley, CA 94720 USA.
   Sinn, Brandon T.; Cavaliere, Dario; Stevenson, Dennis W., New York Bot Garden, Bronx, NY 10458 USA.
   Smith, Barry, Univ Buffalo, Dept Philosophy, Buffalo, NY 14260 USA.
   Qu, Botong; Zhang, Eugene; Todorovic, Sinisa, Oregon State Univ, Sch Elect Engn \& Comp Sci, Corvallis, OR 97331 USA.
   Gkoutos, Georgios, Univ Birmingham, Inst Canc \& Genom Sci, Birmingham B15 2TT, W Midlands, England.
   Doonan, John H., Aberystwyth Univ, Natl Plant Phen Ctr, Inst Biol Environm \& Rural Sci, Aberystwyth SY23 3DA, Dyfed, Wales.
   Sinn, Brandon T., Univ Virginia, Dept Biol, Morgantown, WV 26506 USA.},
DOI = {10.1093/nar/gkx1152},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENE ONTOLOGY; TOOL; ANNOTATION; VOCABULARY; ANATOMY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {jaiswalp@science.oregonstate.edu},
Affiliations = {Oregon State University; Alliance; Bioversity International; United
   States Department of Energy (DOE); Lawrence Berkeley National
   Laboratory; New York Botanical Garden; State University of New York
   (SUNY) System; State University of New York (SUNY) Buffalo; Oregon State
   University; University of Birmingham; UK Research \& Innovation (UKRI);
   Biotechnology and Biological Sciences Research Council (BBSRC);
   Institute of Biological, Environmental, Rural \& Sciences (IBERS);
   Aberystwyth University; University of Virginia},
ResearcherID-Numbers = {Mungall, Chris/I-6006-2019
   Sinn, Brandon T./I-2147-2019
   Jaiswal, Pankaj/H-7599-2016
   Sinn, Brandon/AAW-5177-2021
   Smith, Barry/A-9525-2011
   Gkoutos, Georgios/AAS-9936-2020
   },
ORCID-Numbers = {Mungall, Chris/0000-0002-6601-2165
   Sinn, Brandon T./0000-0002-5596-6895
   Jaiswal, Pankaj/0000-0002-1005-8383
   Smith, Barry/0000-0003-1384-116X
   Gkoutos, Georgios/0000-0002-2061-091X
   Laporte, Marie-Angelique/0000-0002-8461-9745
   Arnaud, Elizabeth/0000-0002-6020-5919
   doonan, john/0000-0001-6027-1919},
Funding-Acknowledgement = {National Science Foundation {[}1340112]; National Human Genome Research
   Institute {[}5U41HG002273-14]; Integrated Breeding Platform; CGIAR Big
   Data in Agriculture; BBSRC {[}BBS/E/W/0012843B, BBS/E/W/10961A01,
   BBS/E/W/10962A01D] Funding Source: UKRI; Biotechnology and Biological
   Sciences Research Council {[}BBS/OS/GC/000011C, BBS/E/W/0012844A,
   BBS/E/W/10961A01, BBS/E/W/10962A01D, BBS/E/W/0012843B] Funding Source:
   researchfish; Medical Research Council {[}HDR-3003] Funding Source:
   researchfish; Direct For Biological Sciences; Division Of Integrative
   Organismal Systems {[}1340112] Funding Source: National Science
   Foundation},
Funding-Text = {National Science Foundation award {[}IOS \#1340112]; National Human
   Genome Research Institute award to the Gene Ontology
   {[}\#5U41HG002273-14] (to C.M., S.C., N.A.D.); Integrated Breeding
   Platform (to E.A., M.A.L.); CGIAR Big Data in Agriculture (to E.A.,
   M.A.L.). Funding for open access charge: National Science Foundation
   {[}IOS \#1340112].},
Number-of-Cited-References = {35},
Times-Cited = {98},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {33},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {FS1QA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000419550700167},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000312893300124,
Author = {Hu, Zhi-Liang and Park, Carissa A. and Wu, Xiao-Lin and Reecy, James M.},
Title = {Animal QTLdb: an improved database tool for livestock animal
   QTL/association data dissemination in the post-genome era},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2013},
Volume = {41},
Number = {D1},
Pages = {D871-D879},
Month = {JAN},
Abstract = {The Animal QTL database (QTLdb; http://www.animalgenome.org/QTLdb) is
   designed to house all publicly available QTL and single-nucleotide
   polymorphism/gene association data on livestock animal species. An
   earlier version was published in the Nucleic Acids Research Database
   issue in 2007. Since then, we have continued our efforts to develop new
   and improved database tools to allow more data types, parameters and
   functions. Our efforts have transformed the Animal QTLdb into a tool
   that actively serves the research community as a quality data repository
   and more importantly, a provider of easily accessible tools and
   functions to disseminate QTL and gene association information. The QTLdb
   has been heavily used by the livestock genomics community since its
   first public release in 2004. To date, there are 5920 cattle, 3442
   chicken, 7451 pigs, 753 sheep and 88 rainbow trout data points in the
   database, and at least 290 publications that cite use of the database.
   The rapid advancement in genomic studies of cattle, chicken, pigs, sheep
   and other livestock animals has presented us with challenges, as well as
   opportunities for the QTLdb to meet the evolving needs of the research
   community. Here, we report our progress over the recent years and
   highlight new functions and services available to the general public.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Hu, ZL (Corresponding Author), Iowa State Univ, Dept Anim Sci, 2255 Kildee Hall, Ames, IA 50011 USA.
   Hu, Zhi-Liang; Park, Carissa A.; Reecy, James M., Iowa State Univ, Dept Anim Sci, Ames, IA 50011 USA.
   Hu, Zhi-Liang; Park, Carissa A.; Reecy, James M., Iowa State Univ, Ctr Integrated Anim Genom, Ames, IA 50011 USA.
   Wu, Xiao-Lin, Univ Wisconsin, Coll Agr \& Life Sci, Dept Meat \& Anim Sci, Madison, WI 53706 USA.},
DOI = {10.1093/nar/gks1150},
ISSN = {0305-1048},
EISSN = {1362-4962},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {zhu@iastate.edu
   jreecy@iastate.edu},
Affiliations = {Iowa State University; Iowa State University; University of Wisconsin
   System; University of Wisconsin Madison},
ResearcherID-Numbers = {li, yihua/JKJ-1325-2023
   },
ORCID-Numbers = {Reecy, James/0000-0003-4602-0990},
Funding-Acknowledgement = {USDA NRSP-8 National Animal Genome Research Program; USDA-NRI
   {[}2007-04187]; USDA-NIFA},
Funding-Text = {The USDA NRSP-8 National Animal Genome Research Program, Bioinformatics
   Coordination Project and partly by the USDA-NRI {[}2007-04187]. Funding
   for open access charge: USDA-NIFA Research Funds to the National
   Research Service Program, NRSP-8, National Animal Genome Research
   Program.},
Number-of-Cited-References = {10},
Times-Cited = {303},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {30},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {062BE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000312893300124},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:001102063800001,
Author = {Castanyer, Roger Creus and Martinez-Fernandez, Silverio and Franch,
   Xavier},
Title = {Which design decisions in AI-enabled mobile applications contribute to
   greener AI?},
Journal = {EMPIRICAL SOFTWARE ENGINEERING},
Year = {2024},
Volume = {29},
Number = {1},
Month = {FEB},
Abstract = {BackgroundThe usage of complex artificial intelligence (AI) models
   demands expensive computational resources. While currently, available
   high-performance computing environments can support such complexity, the
   deployment of AI models in mobile devices, which is an increasing trend,
   is challenging. Environments with low computational resources imply
   limitations in the design decisions during the AI-enabled software
   engineering lifecycle that balance the trade-off between the accuracy
   and the complexity of the mobile applications.ObjectiveOur objective is
   to systematically assess the trade-off between accuracy and complexity
   when deploying complex AI models (e.g. neural networks) to mobile
   devices in pursuit of greener AI solutions. We aim to cover (i) the
   impact of the design decisions on the achievement of high-accuracy and
   low resource-consumption implementations; and (ii) the validation of
   profiling tools for systematically promoting greener AI.MethodWe
   implement neural networks in mobile applications to solve multiple image
   and text classification problems on a variety of benchmark datasets. We
   then profile and model the accuracy, storage weight, and time of CPU
   usage of the AI-enabled applications in operation with respect to their
   design decisions. Finally, we provide an open-source data repository
   following the EMSE open science practices and containing all the
   experimentation, analysis, and reports in our study.ResultsWe find that
   the number of parameters in the AI models makes the time of CPU usage
   scale exponentially in convolutional neural networks and logarithmically
   in fully-connected layers. We also see the storage weight scales
   linearly with the number of parameters, while the accuracy does not. For
   this reason, we argue that a good practice for practitioners is to start
   small and only increase the size of the AI models when their accuracy is
   low. We also find that Residual Networks (ResNets) and Transformers have
   a higher baseline cost in time of CPU usage than simple convolutional
   and recurrent neural networks. Finally, we find that the dataset used
   for experimentation affects both the scaling properties and accuracy of
   the AI models, hence showing that researchers must study the presented
   set of design decisions in each specific problem context.ConclusionsWe
   have depicted an underlying and existing relationship between the design
   of AI models and the performance of the applications that integrate
   these, and we motivate further work and extensions to better
   characterize this complex relationship.},
Publisher = {SPRINGER},
Address = {VAN GODEWIJCKSTRAAT 30, 3311 GZ DORDRECHT, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Castanyer, RC (Corresponding Author), Univ Politecn Cataluna, Barcelona, Spain.
   Castanyer, Roger Creus; Martinez-Fernandez, Silverio; Franch, Xavier, Univ Politecn Cataluna, Barcelona, Spain.},
DOI = {10.1007/s10664-023-10407-7},
Article-Number = {2},
ISSN = {1382-3256},
EISSN = {1573-7616},
Keywords = {AI-enabled applications; Mobile applications; Model accuracy;
   Application performance; Greener AI; Neural networks},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Software Engineering},
Author-Email = {roger.creus@estudiantat.upc.edu
   silverio.martinez@upc.edu
   xavier.franch@upc.edu},
Affiliations = {Universitat Politecnica de Catalunya},
ResearcherID-Numbers = {Franch, Xavier/A-8588-2008
   Creus Castanyer, Roger Creus/ADB-5804-2022
   Martínez-Fernández, Silverio/P-5615-2014
   },
ORCID-Numbers = {Creus Castanyer, Roger Creus/0000-0003-1952-3357
   Martínez-Fernández, Silverio/0000-0001-9928-133X
   Franch, Xavier/0000-0001-9733-8830},
Funding-Acknowledgement = {This work has been partially supported by the GAISSA project
   (TED2021-130923B-I00, which is funded by MCIN/AEI/10.13039/501100011033
   and by the European Union ``NextGenerationEU{''}/PRTR); and, by the
   ``Beatriz Galindo{''} Spanish Program (BEAGAL18/00064).
   {[}TED2021-130923B-I00, MCIN/AEI/10.13039/501100011033]; European Union
   {[}BEAGAL18/00064]},
Funding-Text = {This work has been partially supported by the GAISSA project
   (TED2021-130923B-I00, which is funded by MCIN/AEI/10.13039/501100011033
   and by the European Union ``NextGenerationEU{''}/PRTR); and, by the
   ``Beatriz Galindo{''} Spanish Program (BEAGAL18/00064).},
Number-of-Cited-References = {52},
Times-Cited = {0},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Empir. Softw. Eng.},
Doc-Delivery-Number = {Y0DO7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001102063800001},
OA = {Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001010546200001,
Author = {Sanders, Lauren M. and Chok, Hamed and Samson, Finsam and Acuna, Ana
   Uriarte and Polo, San-Huei Lai and Boyko, Valery and Chen, Yi-Chun and
   Dinh, Marie and Gebre, Samrawit and Galazka, Jonathan M. and Costes,
   Sylvain V. and Saravia-Butler, Amanda M.},
Title = {Batch effect correction methods for NASA GeneLab transcriptomic datasets},
Journal = {FRONTIERS IN ASTRONOMY AND SPACE SCIENCES},
Year = {2023},
Volume = {10},
Month = {JUN 1},
Abstract = {Introduction: RNA sequencing (RNA-seq) data from space biology
   experiments promise to yield invaluable insights into the effects of
   spaceflight on terrestrial biology. However, sample numbers from each
   study are low due to limited crew availability, hardware, and space. To
   increase statistical power, spaceflight RNA-seq datasets from different
   missions are often aggregated together. However, this can introduce
   technical variation or ``batch effects{''}, often due to differences in
   sample handling, sample processing, and sequencing platforms. Several
   computational methods have been developed to correct for technical batch
   effects, thereby reducing their impact on true biological
   signals.Methods: In this study, we combined 7 mouse liver RNA-seq
   datasets from NASA GeneLab (part of the NASA Open Science Data
   Repository) to evaluate several common batch effect correction methods
   (ComBat and ComBat-seq from the sva R package, and Median Polish,
   Empirical Bayes, and ANOVA from the MBatch R package). Principal
   component analysis (PCA) was used to identify library preparation method
   and mission as the primary sources of batch effect among the technical
   variables in the combined dataset. We next quantitatively evaluated the
   ability of each of the indicated methods to correct for each identified
   technical batch variable using the following criteria: BatchQC, PCA,
   dispersion separability criterion, log fold change correlation, and
   differential gene expression analysis. Each batch variable/correction
   method combination was then assessed using a custom scoring approach to
   identify the optimal correction method for the combined dataset, by
   geometrically probing the space of all allowable scoring functions to
   yield an aggregate volume-based scoring measure.Results and Discussion:
   Using the method described for the combined dataset in this study, the
   library preparation variable/ComBat correction method pair out ranked
   the other candidate pairs, suggesting that this combined dataset should
   be corrected for library preparation using the ComBat correction method
   prior to downstream analysis. We describe the GeneLab multi-study
   analysis and visualization portal which will allow users to access the
   publicly available space biology `omics data, select multiple studies to
   combine for analysis, and examine the presence or absence of batch
   effects using multiple metrics. If the user chooses to perform batch
   effect correction, the scoring approach described here can be
   implemented to identify the optimal correction method to use for their
   specific combined dataset prior to analysis.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Saravia-Butler, AM (Corresponding Author), NASA Ames Res Ctr, Moffett Field, CA 94043 USA.
   Saravia-Butler, AM (Corresponding Author), NASA Ames Res Ctr, KBR, Space Biosci Div, Moffett Field, CA 94043 USA.
   Sanders, Lauren M., NASA Ames, Blue Marble Space Inst Sci, Seattle, WA USA.
   Sanders, Lauren M.; Acuna, Ana Uriarte; Polo, San-Huei Lai; Boyko, Valery; Chen, Yi-Chun; Dinh, Marie; Gebre, Samrawit; Galazka, Jonathan M.; Costes, Sylvain V.; Saravia-Butler, Amanda M., NASA Ames Res Ctr, Moffett Field, CA 94043 USA.
   Chok, Hamed, GeneLab Multi Anal Working Grp, Houston, TX USA.
   Samson, Finsam, Stanford Univ, Dept Comp Sci, Stanford, CA USA.
   Acuna, Ana Uriarte; Polo, San-Huei Lai; Chen, Yi-Chun; Saravia-Butler, Amanda M., NASA Ames Res Ctr, KBR, Space Biosci Div, Moffett Field, CA 94043 USA.
   Boyko, Valery, NASA Ames Res Ctr, Bionet Corp, Moffett Field, CA USA.
   Dinh, Marie, Logyx LLC, Mountain View, CA USA.},
DOI = {10.3389/fspas.2023.1200132},
Article-Number = {1200132},
ISSN = {2296-987X},
Keywords = {RNA-seq; batch effect correction; NASA genelab; space biology;
   transcriptomics; combat; combat-seq; MBatch},
Keywords-Plus = {SPACEFLIGHT; EXPRESSION; MUSCLES},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {amanda.m.saravia-butler@nasa.gov},
Affiliations = {National Aeronautics \& Space Administration (NASA); NASA Ames Research
   Center; National Aeronautics \& Space Administration (NASA); NASA Ames
   Research Center; Stanford University; National Aeronautics \& Space
   Administration (NASA); NASA Ames Research Center; National Aeronautics
   \& Space Administration (NASA); NASA Ames Research Center},
Funding-Acknowledgement = {NASA Space Biology Program within the NASA Science Mission Directorate's
   (SMD) Biological and Physical Sciences (BPS) Division},
Funding-Text = {This work was funded by the NASA Space Biology Program within the NASA
   Science Mission Directorate's (SMD) Biological and Physical Sciences
   (BPS) Division.},
Number-of-Cited-References = {39},
Times-Cited = {0},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Front. Astron. Space Sci.},
Doc-Delivery-Number = {J6FG1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001010546200001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000323603200011,
Author = {Xia, Jianguo and Fjell, Christopher D. and Mayer, Matthew L. and Pena,
   Olga M. and Wishart, David S. and Hancock, Robert E. W.},
Title = {INMEX-a web-based tool for integrative meta-analysis of expression data},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2013},
Volume = {41},
Number = {W1},
Pages = {W63-W70},
Month = {JUL},
Abstract = {The widespread applications of various `omics' technologies in
   biomedical research together with the emergence of public data
   repositories have resulted in a plethora of data sets for almost any
   given physiological state or disease condition. Properly combining or
   integrating these data sets with similar basic hypotheses can help
   reduce study bias, increase statistical power and improve overall
   biological understanding. However, the difficulties in data management
   and the complexities of analytical approaches have significantly limited
   data integration to enable meta-analysis. Here, we introduce integrative
   meta-analysis of expression data (INMEX), a user-friendly web-based tool
   designed to support meta-analysis of multiple gene-expression data sets,
   as well as to enable integration of data sets from gene expression and
   metabolomics experiments. INMEX contains three functional modules. The
   data preparation module supports flexible data processing, annotation
   and visualization of individual data sets. The statistical analysis
   module allows researchers to combine multiple data sets based on
   P-values, effect sizes, rank orders and other features. The significant
   genes can be examined in functional analysis module for enriched Gene
   Ontology terms or Kyoto Encyclopedia of Genes and Genomes (KEGG)
   pathways, or expression profile visualization. INMEX has built-in
   support for common gene/metabolite identifiers (IDs), as well as 45
   popular microarray platforms for human, mouse and rat. Complex
   operations are performed through a user-friendly web interface in a
   step-by-step manner. INMEX is freely available at http://www.inmex.ca.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Hancock, REW (Corresponding Author), Univ British Columbia, Dept Microbiol \& Immunol, Vancouver, BC V6T 1Z3, Canada.
   Xia, Jianguo; Mayer, Matthew L.; Pena, Olga M.; Hancock, Robert E. W., Univ British Columbia, Dept Microbiol \& Immunol, Vancouver, BC V6T 1Z3, Canada.
   Xia, Jianguo; Mayer, Matthew L.; Pena, Olga M.; Hancock, Robert E. W., Univ British Columbia, Ctr Microbial Dis \& Immun Res, Vancouver, BC V6T 1Z4, Canada.
   Fjell, Christopher D., Univ British Columbia, James Hogg Res Ctr, Vancouver, BC V6Z 1Y6, Canada.
   Wishart, David S., Univ Alberta, Dept Comp Sci, Edmonton, AB T6G 2E8, Canada.
   Wishart, David S., Univ Alberta, Dept Biol Sci, Edmonton, AB T6G 2E8, Canada.
   Hancock, Robert E. W., Wellcome Trust Sanger Inst, Hinxton CB10 1SA, England.},
DOI = {10.1093/nar/gkt338},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MICROARRAY METAANALYSIS; R PACKAGE; METABOLOMICS; GENES;
   TRANSCRIPTOMICS; VISUALIZATION; METABOANALYST; SERVER},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {bob@hancocklab.ubc.ca},
Affiliations = {University of British Columbia; University of British Columbia;
   University of British Columbia; University of Alberta; University of
   Alberta; Wellcome Trust Sanger Institute},
ResearcherID-Numbers = {Xia, Jianguo/Z-1935-2019
   Hancock, Robert E. W./E-1145-2013
   Wishart, David Scott/ABI-3181-2020
   },
ORCID-Numbers = {Xia, Jianguo/0000-0003-2040-2624
   Hancock, Robert E. W./0000-0001-5989-8503
   Fjell, Christopher/0000-0001-6304-2628
   Wishart, David S/0000-0002-3207-2434},
Funding-Acknowledgement = {Canadian Institutes for Health Research; Canadian Institutes of Health
   Research; Killam Postdoctoral Research Fellowship},
Funding-Text = {Funding to support this research was obtained from the Canadian
   Institutes for Health Research. J. Xia was supported by a Canadian
   Institutes of Health Research Postdoctoral Fellowship and Killam
   Postdoctoral Research Fellowship. REWH holds a Canada Research Chair.
   Funding for open access charge: Canadian Institutes of Health Research.},
Number-of-Cited-References = {43},
Times-Cited = {127},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {27},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {207MC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000323603200011},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000967984600001,
Author = {Lysko, Andrzej and Mackow, Witold and Forczmanski, Pawel and Terefenko,
   Pawel and Giza, Andrzej and Sledziowski, Jakub and Stepien, Grzegorz and
   Tomczak, Arkadiusz},
Title = {CCMORPH-Coastal Cliffs Morphology Analysis Toolbox},
Journal = {SOFTWAREX},
Year = {2023},
Volume = {22},
Month = {MAY},
Abstract = {The Coastal Cliffs Morphology Analysis (CCMORPH) Toolbox is a collection
   of PYTHON scripts and a JavaScript tool to produce georectified
   information specifically tailored for the generation and quantitative
   analysis of coastal cliffs' morphology. Although experts have employed
   numerous methods to extract coastal indicators from digital elevation
   models, most do not enable software code to repeat the proposed
   processes. Here, we provide an easily accessible software solution that
   demonstrates how to automatically extract line indicators from digital
   elevation models using different scientific methodologies and generate
   comparable datasets representing coastal cliff dynamics. (c) 2023 The
   Author(s). Published by Elsevier B.V. This is an open access article
   under the CC BY license (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Lysko, A (Corresponding Author), West Pomeranian Univ Technol, Fac Comp Sci \& Informat Technol, Zolnierska 49, PL-71210 Szczecin, Poland.
   Lysko, Andrzej; Mackow, Witold; Forczmanski, Pawel, West Pomeranian Univ Technol, Fac Comp Sci \& Informat Technol, Zolnierska 49, PL-71210 Szczecin, Poland.
   Terefenko, Pawel; Giza, Andrzej; Sledziowski, Jakub, Univ Szczecin, Inst Marine \& Environm Sci, Mickiewicza 16, PL-70383 Szczecin, Poland.
   Stepien, Grzegorz; Tomczak, Arkadiusz, Maritime Univ Szczecin, Fac Nav, Waly Chrobrego 1 2, PL-70500 Szczecin, Poland.},
DOI = {10.1016/j.softx.2023.101386},
EarlyAccessDate = {APR 2023},
Article-Number = {101386},
ISSN = {2352-7110},
Keywords = {Python; JavaScript; Cliffs; Coastline morphology indicators; Baltic
   Coastal Monitoring Team},
Keywords-Plus = {AUTOMATIC DELINEATION; BEACH; LIDAR; UAV; PHOTOGRAMMETRY; COASTLINES;
   EROSION; TOP},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Software Engineering},
Author-Email = {andrzej.lysko@zut.edu.pl},
Affiliations = {West Pomeranian University of Technology; University of Szczecin;
   Maritime University of Szczecin},
ResearcherID-Numbers = {Giza, Andrzej/HTL-4146-2023
   Forczmanski, Pawel/L-1055-2013
   },
ORCID-Numbers = {Giza, Andrzej/0000-0002-5459-9261
   Sledziowski, Jakub/0000-0001-9359-7907
   Forczmanski, Pawel/0000-0002-3618-9146
   Lysko, Andrzej/0000-0001-8900-0100
   Tomczak, Arkadiusz/0000-0003-1275-2659},
Funding-Acknowledgement = {National Science Centre Poland; European Regional Development Fund -
   National Science Centre, Poland {[}2020/39/B/ST10/01122]; European Union
   {[}POPC.02.03.01- 00-0062/18-00]},
Funding-Text = {The authors declare the following financial interests/personal
   relationships which may be considered as potential competing interests:
   Terefenko reports financial support was provided by National Science
   Centre Poland. Giza reports financial support was provided by European
   Regional Development Fund. This research was funded by the National
   Science Centre, Poland, through the project ?Influence of surf zone and
   beach morphology on coastal cliff retreat - INSUMOR?, project number
   2020/39/B/ST10/01122. The data repository used for software testing was
   funded by the European Union through the project ?The Oceanographic Data
   and Information System eCUDO.pl?- contract no. POPC.02.03.01-
   00-0062/18-00 realized within the Operational Programme Digi- tal Poland
   2014-2020 Fund.},
Number-of-Cited-References = {38},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {SoftwareX},
Doc-Delivery-Number = {D3TM1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000967984600001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000276399100024,
Author = {Zhang, Yan and Lv, Jie and Liu, Hongbo and Zhu, Jiang and Su, Jianzhong
   and Wu, Qiong and Qi, Yunfeng and Wang, Fang and Li, Xia},
Title = {HHMD: the human histone modification database},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2010},
Volume = {38},
Number = {1},
Pages = {D149-D154},
Month = {JAN},
Abstract = {Histone modifications play important roles in chromatin remodeling, gene
   transcriptional regulation, stem cell maintenance and differentiation.
   Alterations in histone modifications may be linked to human diseases
   especially cancer. Histone modifications including methylation,
   acetylation and ubiquitylation probed by ChIP-seq, ChIP-chip and qChIP
   have become widely available. Mining and integration of histone
   modification data can be beneficial to novel biological discoveries.
   There has been no comprehensive data repository that is exclusive for
   human histone modifications. Therefore, we developed a relatively
   comprehensive database for human histone modifications. Human Histone
   Modification Database (HHMD, http://bioinfo.hrbmu.edu.cn/hhmd) focuses
   on the storage and integration of histone modification datasets that
   were obtained from laboratory experiments. The latest release of HHMD
   incorporates 43 location-specific histone modifications in human. To
   facilitate data extraction, flexible search options are built in HHMD.
   It can be searched by histone modification, gene ID, functional
   categories, chromosome location and cancer name. HHMD also includes a
   user-friendly visualization tool named HisModView, by which genome-wide
   histone modification map can be shown. HisModView facilitates the
   acquisition and visualization of histone modifications. The database
   also has manually curated information of histone modification
   dysregulation in nine human cancers.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Li, X (Corresponding Author), Harbin Med Univ, Coll Bioinformat Sci \& Technol, Harbin 150081, Peoples R China.
   Zhang, Yan; Lv, Jie; Liu, Hongbo; Zhu, Jiang; Su, Jianzhong; Qi, Yunfeng; Wang, Fang; Li, Xia, Harbin Med Univ, Coll Bioinformat Sci \& Technol, Harbin 150081, Peoples R China.
   Wu, Qiong, Harbin Inst Technol, Dept Life Sci \& Engn, Harbin 150001, Peoples R China.},
DOI = {10.1093/nar/gkp968},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {FOLD-CONTAINING PROTEINS; EMBRYONIC STEM-CELLS; DNA METHYLATION; HUMAN
   GENOME; CANCER EPIGENOMICS; RESOURCE; EPIGENETICS; ANNOTATION; PATTERNS;
   THERAPY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {yanyou1225@yahoo.com.cn
   lixia@hrbmu.edu.cn},
Affiliations = {Harbin Medical University; Harbin Institute of Technology},
ResearcherID-Numbers = {wu, qiong/GRY-4672-2022
   li, xia/HHZ-7468-2022
   Lyu, Jie/AAP-4077-2020
   Liu, Hongbo/M-2162-2015},
ORCID-Numbers = {Lyu, Jie/0000-0002-6530-5257
   Liu, Hongbo/0000-0002-0733-8616},
Funding-Acknowledgement = {National Natural Science Foundation of China {[}30871394]; National High
   Tech Development Project of China, the 863 Program {[}2007AA02Z329];
   National Basic Research Program of China, the 973 Program
   {[}2008CB517302]; Natural Science Foundation of Heilongjiang Province
   {[}D2007-35]; Innovation and Technology special Fund for researchers of
   Harbin {[}RC2007LX003004]},
Funding-Text = {National Natural Science Foundation of China (Grant No. 30871394); the
   National High Tech Development Project of China, the 863 Program (Grant
   No. 2007AA02Z329); the National Basic Research Program of China, the 973
   Program (Grant No. 2008CB517302); the Natural Science Foundation of
   Heilongjiang Province (Grant No. D2007-35); the Innovation and
   Technology special Fund for researchers of Harbin (Grant No.
   RC2007LX003004). Funding for open access charge: National Natural
   Science Foundation of China (Grant No. 30871394).},
Number-of-Cited-References = {40},
Times-Cited = {62},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {26},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {579TV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000276399100024},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000285831700150,
Author = {Ahmed, Jessica and Meinel, Thomas and Dunkel, Mathias and Murgueitio,
   Manuela S. and Adams, Robert and Blasse, Corinna and Eckert, Andreas and
   Preissner, Saskia and Preissner, Robert},
Title = {CancerResource: a comprehensive database of cancer-relevant proteins and
   compound interactions supported by experimental knowledge},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2011},
Volume = {39},
Number = {1},
Pages = {D960-D967},
Month = {JAN},
Abstract = {During the development of methods for cancer diagnosis and treatment, a
   vast amount of information is generated. Novel cancer target proteins
   have been identified and many compounds that activate or inhibit
   cancer-relevant target genes have been developed. This knowledge is
   based on an immense number of experimentally validated compound-target
   interactions in the literature, and excerpts from literature text mining
   are spread over numerous data sources. Our own analysis shows that the
   overlap between important existing repositories such as Comparative
   Toxicogenomics Database (CTD), Therapeutic Target Database (TTD),
   Pharmacogenomics Knowledge Base (PharmGKB) and DrugBank as well as
   between our own literature mining for cancer-annotated entries is
   surprisingly small. In order to provide an easy overview of interaction
   data, it is essential to integrate this information into a single,
   comprehensive data repository. Here, we present CancerResource, a
   database that integrates cancer-relevant relationships of compounds and
   targets from (i) our own literature mining and (ii) external resources
   complemented with (iii) essential experimental and supporting
   information on genes and cellular effects. In order to facilitate an
   overview of existing and supporting information, a series of novel
   information connections have been established. CancerResource addresses
   the spectrum of research on compound-target interactions in natural
   sciences as well as in individualized medicine; CancerResource is
   available at: http://bioinformatics.charite.de/cancerresource/.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Preissner, R (Corresponding Author), Charite, Struct Bioinformat Grp, Inst Physiol, Thielallee 71, D-14195 Berlin, Germany.
   Ahmed, Jessica; Meinel, Thomas; Dunkel, Mathias; Murgueitio, Manuela S.; Adams, Robert; Blasse, Corinna; Eckert, Andreas; Preissner, Saskia; Preissner, Robert, Charite, Struct Bioinformat Grp, Inst Physiol, D-14195 Berlin, Germany.},
DOI = {10.1093/nar/gkq910},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENE-EXPRESSION; RESOURCE; TOOL},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {robert.preissner@charite.de},
Affiliations = {Free University of Berlin; Humboldt University of Berlin; Charite
   Universitatsmedizin Berlin},
ORCID-Numbers = {preissner, robert/0000-0002-2407-1087
   Dunkel, Mathias/0000-0002-6642-483X},
Funding-Acknowledgement = {International Research Training Group IRTG (Genomics and Systems Biology
   of Molecular Networks) Deutsche Krebshilfe; Deutsche
   Forschungsgemeinschaft DFG; Federal Ministry of Education and Research
   BMBF; European Union EU},
Funding-Text = {The International Research Training Group IRTG (Genomics and Systems
   Biology of Molecular Networks) Deutsche Krebshilfe; Deutsche
   Forschungsgemeinschaft DFG; Federal Ministry of Education and Research
   BMBF (MedSys Project); European Union EU (SynSys Project). Funding for
   open access charge: DFG, BMBF, EU.},
Number-of-Cited-References = {36},
Times-Cited = {62},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {701PA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000285831700150},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000713240900001,
Author = {Enrique Puliafito, S. and Bolano-Ortiz, Tomas R. and Fernandez, Rafael
   P. and Berna, Lucas L. and Pascual-Flores, Romina M. and Urquiza,
   Josefina and Lopez-Norena, I, Ana and Tames, Maria F.},
Title = {High-resolution seasonal and decadal inventory of anthropogenic
   gas-phase and particle emissions for Argentina},
Journal = {EARTH SYSTEM SCIENCE DATA},
Year = {2021},
Volume = {13},
Number = {10},
Pages = {5027-5069},
Month = {OCT 29},
Abstract = {This work presents the integration of a gas-phase and particulate
   atmospheric emission inventory (AEI) for Argentina in high spatial
   resolution (0.025 degrees x0.025 degrees; approx. 2.5 km x 2.5 km)
   considering monthly variability from 1995 to 2020. The new inventory,
   called GEAA-AEIv3.0M, includes the following activities: energy
   production, fugitive emissions from oil and gas production, industrial
   fuel consumption and production, transport (road, maritime, and air),
   agriculture, livestock production, manufacturing, residential,
   commercial, and biomass and agricultural waste burning. The following
   species, grouped by atmospheric reactivity, are considered: (i)
   greenhouse gases (GHGs) - CO2, CH4, and N2O; (ii) ozone precursors - CO,
   NOx (NO+NO2), and non-methane volatile organic compounds (NMVOCs); (iii)
   acidifying gases - NH3 and SO2; and (iv) particulate matter (PM) - PM10,
   PM2.5, total suspended particles (TSPs), and black carbon (BC). The main
   objective of the GEAA-AEIv3.0M high-resolution emission inventory is to
   provide temporally resolved emission maps to support air quality and
   climate modeling oriented to evaluate pollutant mitigation strategies by
   local governments. This is of major concern, especially in countries
   where air quality monitoring networks are scarce, and the development of
   regional and seasonal emissions inventories would result in remarkable
   improvements in the time and space chemical prediction achieved by air
   quality models.
   Despite distinguishing among different sectoral and activity databases
   as well as introducing a novel spatial distribution approach based on
   census radii, our high-resolution GEAA-AEIv3.0M shows equivalent
   national-wide total emissions compared to the Third National
   Communication of Argentina (TNCA), which compiles annual GHG emissions
   from 1990 through 2014 (agreement within +/- 7.5 \%). However, the
   GEAA-AEIv3.0M includes acidifying gases and PM species not considered in
   TNCA. Temporal comparisons were also performed against two international
   databases: Community Emissions Data System (CEDS) and EDGAR HTAPv5.0 for
   several pollutants; for EDGAR it also includes a spatial comparison.
   The agreement was acceptable within less than 30 \% for most of the
   pollutants and activities, although a >90 \% discrepancy was obtained
   for methane from fuel production and fugitive emissions and >120 \% for
   biomass burning. Finally, the updated seasonal series clearly showed the
   pollution reduction due to the COVID-19 lockdown during the first
   quarter of year 2020 with respect to same months in previous years.
   Through an open-access data repository, we present the GEAA-AEIv3.0M
   inventory as the largest and more detailed spatial resolution dataset
   for the Argentine Republic, which includes monthly gridded emissions for
   12 species and 15 stors between 1995 and 2020.},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Puliafito, SE (Corresponding Author), Natl Technol Univ FRM UTN, Res Grp Atmospher \& Environm Studies GEAA, Mendoza Reg Fac, RA-5500 Mendoza, Argentina.
   Puliafito, SE (Corresponding Author), Natl Sci \& Tech Res Council CONICET, RA-5500 Mendoza, Argentina.
   Enrique Puliafito, S.; Bolano-Ortiz, Tomas R.; Berna, Lucas L.; Pascual-Flores, Romina M.; Urquiza, Josefina; Lopez-Norena, Ana, I; Tames, Maria F., Natl Technol Univ FRM UTN, Res Grp Atmospher \& Environm Studies GEAA, Mendoza Reg Fac, RA-5500 Mendoza, Argentina.
   Enrique Puliafito, S.; Bolano-Ortiz, Tomas R.; Fernandez, Rafael P.; Pascual-Flores, Romina M.; Urquiza, Josefina; Lopez-Norena, Ana, I; Tames, Maria F., Natl Sci \& Tech Res Council CONICET, RA-5500 Mendoza, Argentina.
   Berna, Lucas L., Natl Agcy Sci \& Technol Promot ANPCyT, RA-1675 Buenos Aires, DF, Argentina.
   Fernandez, Rafael P.; Lopez-Norena, Ana, I, Natl Univ Cuyo FCEN UNCuyo, Sch Nat Sci, RA-5501 Mendoza, Argentina.
   Fernandez, Rafael P., Inst Interdisciplinary Sci ICB CONICET, RA-5501 Mendoza, Argentina.
   Bolano-Ortiz, Tomas R., Univ Tecn Federico Santa Maria USM, Ctr Environm Technol CETAM, Valparaiso 46383, Chile.},
DOI = {10.5194/essd-13-5027-2021},
ISSN = {1866-3508},
EISSN = {1866-3516},
Keywords-Plus = {AIR-QUALITY; METHANE EMISSIONS; CLIMATE-CHANGE; OZONE; SECTOR; AERMOD;
   SENSITIVITY; VALIDATION; AEROSOLS; CALPUFF},
Research-Areas = {Geology; Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary; Meteorology \& Atmospheric Sciences},
Author-Email = {epuliafito@fim.utn.edu},
Affiliations = {Centro Nacional Patagonico (CENPAT)},
ResearcherID-Numbers = {Bolaño-Ortiz, Tomás R./AAX-9605-2020
   Liu, Hai-Ying/P-5557-2014
   TAMES, María Florencia/JFA-7388-2023
   },
ORCID-Numbers = {Bolaño-Ortiz, Tomás R./0000-0002-0033-6001
   Liu, Hai-Ying/0000-0001-8667-3465
   TAMES, María Florencia/0000-0003-3304-3376
   Berna Pena, Lucas Luciano/0000-0003-0407-6726
   Fernandez, Rafael Pedro/0000-0002-4114-5500
   PULIAFITO, SALVADOR ENRIQUE/0000-0001-9085-6870},
Funding-Acknowledgement = {Universidad Tecnologica Nacional (UTN) (National Technological
   University); Consejo Nacional de Investigaciones Cientificas y Tecnicas
   (CONICET) (National Council for Scientific and Technical Investigations)},
Funding-Text = {The authors would like to thank Universidad Tecnologica Nacional (UTN)
   (National Technological University) and Consejo Nacional de
   Investigaciones Cientificas y Tecnicas (CONICET) (National Council for
   Scientific and Technical Investigations) for supporting research
   activities.},
Number-of-Cited-References = {76},
Times-Cited = {6},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {21},
Journal-ISO = {Earth Syst. Sci. Data},
Doc-Delivery-Number = {WP6LO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000713240900001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000692793000025,
Author = {Thompson, Lindsay A. and Gurka, Matthew J. and Filipp, Stephanie L. and
   Schatz, Desmond A. and Mercado, Rebeccah E. and Ostrov, David A. and
   Atkinson, Mark A. and Rasmussen, Sonja A.},
Title = {The influence of selection bias on identifying an association between
   allergy medication use and SARS-CoV-2 infection},
Journal = {ECLINICALMEDICINE},
Year = {2021},
Volume = {37},
Month = {JUL},
Abstract = {Background: Medications to prevent and treat SARS-CoV-2 infection are
   needed to complement emerging vaccinations. Recent in vitro and
   electronic health record (EHR) studies suggested that certain allergy
   medi-cations could prevent SARS-CoV-2 infection. We sought to carefully
   examine the potential selection bias associated with utilizing EHRs in
   these settings. Methods: We analyzed associations of three allergy
   medications (cetirizine, diphenhydramine or hydroxy-zine) with testing
   negative for SARS-CoV-2, measuring the potential effect of selection
   bias on these associa-tions. We used a retrospective cohort of EHR data
   from 230,376 patients (18 years+) who visited outpatient clinicians in a
   single, large academic center at least once but were never hospitalized
   (10/1/2019-6/1/2020). Main exposures included EHR documentation of three
   allergy medications and allergy, with an intermediate outcome of receipt
   of a SARS-CoV-2 test, and the primary outcome as testing negative.
   Findings: SARS-CoV-2 testing rates varied by sex, age, race/ethnicity
   and insurance. Increasing age and public insurance were associated with
   a higher adjusted odds of test negativity, while being Black or Hispanic
   was sig-nificantly associated with test positivity. Allergy diagnosis
   and use of any of three allergy medications were each associated with a
   higher likelihood of receiving a test (e.g. diphenhydramine -Odds Ratio
   (OR) 2.99, 95\% Confi-dence Interval (CI) 2.73, 3.28; cetirizine 1.75
   (95\% CI 1.60, 1.92)). Among those tested, only use of diphenhydra-mine
   was associated with a negative SARS-CoV-2 test (adjusted OR = 2.23, 95\%
   CI 1.10, 4.55). However, analyses revealed that selection bias may be
   responsible for the apparent protective effect of diphenhydramine.
   Interpretation: Diphenhydramine use was associated with more SARS-CoV-2
   testing and subsequent higher odds for negative tests. While EHR-based
   observational studies can inform a need for interventional trials, this
   study revealed limitations of EHR data. The finding that diphenhydramine
   documentation conferred a higher odds of testing negative for SARS-CoV-2
   must be interpreted with caution due to probable selection bias.
   Abbreviations: SARS-CoV-2, ACE2, COVID-19, EHR Funding: This study
   received University of Florida Children's Miracle Network funding to
   support the costs of extracting and preparing a limited data set from
   the University of Florida Integrated Data repository. (c) 2021 The
   Author(s). Published by Elsevier Ltd. This is an open access article
   under the CC BY-NC-ND license
   (http://creativecommons.org/licenses/by-nc-nd/4.0/)},
Publisher = {ELSEVIER},
Address = {RADARWEG 29a, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Thompson, LA (Corresponding Author), Univ Florida, Coll Med, Dept Pediat, Gainesville, FL USA.
   Thompson, LA (Corresponding Author), Univ Florida, Coll Med, Dept Hlth Outcomes \& Biomed Informat, Gainesville, FL USA.
   Thompson, Lindsay A.; Gurka, Matthew J.; Schatz, Desmond A.; Mercado, Rebeccah E.; Atkinson, Mark A.; Rasmussen, Sonja A., Univ Florida, Coll Med, Dept Pediat, Gainesville, FL USA.
   Thompson, Lindsay A.; Gurka, Matthew J.; Filipp, Stephanie L., Univ Florida, Coll Med, Dept Hlth Outcomes \& Biomed Informat, Gainesville, FL USA.
   Ostrov, David A.; Atkinson, Mark A., Univ Florida, Coll Med, Dept Pathol, Gainesville, FL USA.
   Rasmussen, Sonja A., Univ Florida, Coll Publ Hlth \& Hlth Profess, Dept Epidemiol, Gainesville, FL USA.
   Rasmussen, Sonja A., Univ Florida, Coll Med, Dept Epidemiol, Gainesville, FL USA.
   Rasmussen, Sonja A., Univ Florida, Coll Med, Dept Obstet \& Gynecol, Gainesville, FL USA.},
DOI = {10.1016/j.eclinm.2021.100936},
EarlyAccessDate = {JUL 2021},
Article-Number = {100936},
EISSN = {2589-5370},
Keywords = {Observational study; Selection bias; COVID-19; SARS-CoV-2},
Keywords-Plus = {PRACTICES INTERIM RECOMMENDATION; UNITED-STATES; ADVISORY-COMMITTEE;
   COVID-19 VACCINE; IDENTIFICATION},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {lathom@ufl.edu},
Affiliations = {State University System of Florida; University of Florida; State
   University System of Florida; University of Florida; State University
   System of Florida; University of Florida; State University System of
   Florida; University of Florida; State University System of Florida;
   University of Florida; State University System of Florida; University of
   Florida},
ORCID-Numbers = {Thompson, Lindsay A./0000-0002-9066-5131},
Funding-Acknowledgement = {University of Florida Children's Miracle Network},
Funding-Text = {The University of Florida Children's Miracle Network partially funded
   this study.},
Number-of-Cited-References = {31},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {EClinicalMedicine},
Doc-Delivery-Number = {UL6XY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000692793000025},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000451246100035,
Author = {Race, Alan M. and Roempp, Andreas},
Title = {Error-Free Data Visualization and Processing through imzML and mzML
   Validation},
Journal = {ANALYTICAL CHEMISTRY},
Year = {2018},
Volume = {90},
Number = {22},
Pages = {13378-13384},
Month = {NOV 20},
Abstract = {Open data formats are key to facilitating data processing, sharing, and
   integration. The imzML format (http://imzml.org/) has drastically
   improved these aspects of mass spectrometry imaging data. Efficient
   processing of data depends on data sets which are consistent and adhere
   to the specifications; however, this is not always the case. Here we
   present a validation tool for data stored in both imzML and the HUPO-PSI
   mass spectrometery counterpart, mzML, to identify any deviations from
   the published (i)mzML standard which could cause issues for the user
   when visualizing or processing data. The tool is released in two forms,
   a graphical user interface (GUI) for ease of use, and a command line
   version to fit into existing workflows and pipelines. When certain known
   issues are encountered, such as the presence of negative values for the
   location of the binary data, the validator resolves the issue
   automatically upon saving. The GUI version of the validator also allows
   editing of the metadata included within the (i)mzML files in order to
   resolve inconsistencies. We also present a means of performing
   conditional validation on the metadata within (i)mzML files, where
   user-defined rules are validated against depending on whether specific
   metadata are present (or not). For example, if the MALDI term is
   present, then additional rules related to MALDI (such as the requirement
   of inclusion of laser parameters) can be validated against this. This
   enables a flexible and more thorough automated validation of (i)mzML
   data. Such a system is necessary for validating data against more
   comprehensive sets of metadata such as minimum reporting guidelines or
   metadata requirements prior to submission and acceptance of data to data
   repositories. We demonstrate how this tool can be used to validate
   against the proposed minimum reporting guidelines in MSI as well as
   institute specific metadata criteria. The validator tool is endorsed for
   validation of imzML (http://imzml.org/) and mzML
   (http://www.psidev.info/mzml) and is made available through the
   respective Web sites. The validator is also released as open source
   under Mozilla Public License 2.0 at
   https://gitlab.com/imzML/imzMLValidator.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Race, AM; Römpp, A (Corresponding Author), Univ Bayreuth, Chair Bioanalyt Sci \& Food Anal, D-95447 Bayreuth, Germany.
   Race, Alan M.; Roempp, Andreas, Univ Bayreuth, Chair Bioanalyt Sci \& Food Anal, D-95447 Bayreuth, Germany.},
DOI = {10.1021/acs.analchem.8b03059},
ISSN = {0003-2700},
EISSN = {1520-6882},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Analytical},
Author-Email = {alan.race@uni-bayreuth.de
   andreas.roempp@uni-bayreuth.de},
Affiliations = {University of Bayreuth},
ResearcherID-Numbers = {Race, Alan/L-3732-2019
   },
ORCID-Numbers = {Race, Alan/0000-0001-8996-2641},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft {[}DFG RO 3421/6-1];
   TechnologieAllianzOberfranken (TAO)},
Funding-Text = {The authors gratefully acknowledge financial support from Deutsche
   Forschungsgemeinschaft (DFG RO 3421/6-1) and
   TechnologieAllianzOberfranken (TAO).},
Number-of-Cited-References = {20},
Times-Cited = {5},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {17},
Journal-ISO = {Anal. Chem.},
Doc-Delivery-Number = {HB7GS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000451246100035},
DA = {2024-01-15},
}

@article{ WOS:000371261700062,
Author = {Vizcaino, Juan Antonio and Csordas, Attila and del-Toro, Noemi and
   Dianes, Jose A. and Griss, Johannes and Lavidas, Ilias and Mayer,
   Gerhard and Perez-Riverol, Yasset and Reisinger, Florian and Ternent,
   Tobias and Xu, Qing-Wei and Wang, Rui and Hermjakob, Henning},
Title = {2016 update of the PRIDE database and its related tools},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2016},
Volume = {44},
Number = {D1},
Pages = {D447-D456},
Month = {JAN 4},
Abstract = {The PRoteomics IDEntifications (PRIDE) database is one of the
   world-leading data repositories of mass spectrometry (MS)-based
   proteomics data. Since the beginning of 2014, PRIDE Archive
   (http://www.ebi.ac.uk/pride/archive/) is the new PRIDE archival system,
   replacing the original PRIDE database. Here we summarize the
   developments in PRIDE resources and related tools since the previous
   update manuscript in the Database Issue in 2013. PRIDE Archive
   constitutes a complete redevelopment of the original PRIDE, comprising a
   new storage backend, data submission system and web interface, among
   other components. PRIDE Archive supports the most-widely used PSI
   (Proteomics Standards Initiative) data standard formats (mzML and
   mzIdentML) and implements the data requirements and guidelines of the
   ProteomeXchange Consortium. The wide adoption of ProteomeXchange within
   the community has triggered an unprecedented increase in the number of
   submitted data sets (around 150 data sets per month). We outline some
   statistics on the current PRIDE Archive data contents. We also report on
   the status of the PRIDE related stand-alone tools: PRIDE Inspector,
   PRIDE Converter 2 and the ProteomeXchange submission tool. Finally, we
   will give a brief update on the resources under development `PRIDE
   Cluster' and `PRIDE Proteomes', which provide a complementary view and
   quality-scored information of the peptide and protein identification
   data available in PRIDE Archive.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Vizcaíno, JA (Corresponding Author), European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Vizcaino, Juan Antonio; Csordas, Attila; del-Toro, Noemi; Dianes, Jose A.; Griss, Johannes; Lavidas, Ilias; Mayer, Gerhard; Perez-Riverol, Yasset; Reisinger, Florian; Ternent, Tobias; Xu, Qing-Wei; Wang, Rui; Hermjakob, Henning, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Griss, Johannes, Med Univ Vienna, Div Immunol Allergy \& Infect Dis, Dept Dermatol, Vienna, Austria.
   Mayer, Gerhard, Ruhr Univ Bochum, MPC, D-44801 Bochum, Germany.
   Xu, Qing-Wei, Hubei Univ Educ, Dept Comp Sci \& Technol, Wuhan, Peoples R China.
   Hermjakob, Henning, Natl Ctr Prot Sci, Beijing, Peoples R China.},
DOI = {10.1093/nar/gkv1145},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PROTEOMICS DATA; PEPTIDE IDENTIFICATION; PUBLIC REPOSITORY; DATA
   SUBMISSION; JAVA INTERFACE; PROTEIN; PROTEOMEXCHANGE; STANDARD; API;
   REANALYSIS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {juan@ebi.ac.uk},
Affiliations = {Wellcome Trust Sanger Institute; European Molecular Biology Laboratory
   (EMBL); Medical University of Vienna; Ruhr University Bochum; Hubei
   University of Education},
ResearcherID-Numbers = {Perez-Riverol, Yasset/H-2873-2019
   Vizcaino, Juan Antonio/C-3691-2009
   Hermjakob, Henning/AFM-3497-2022
   },
ORCID-Numbers = {Perez-Riverol, Yasset/0000-0001-6579-6941
   Vizcaino, Juan Antonio/0000-0002-3905-4335
   Hermjakob, Henning/0000-0001-8479-0262
   del Toro Ayllon, Noemi/0000-0001-5272-7613
   Griss, Johannes/0000-0003-2206-9511
   Lavidas, Ilias/0000-0002-8060-7595
   Dianes, Jose A/0000-0002-5904-9269
   Ternent, Tobias/0000-0003-0279-7335
   Mayer, Gerhard/0000-0002-1767-2343},
Funding-Acknowledgement = {Wellcome Trust {[}WT085949MA, WT101477MA]; EU {[}260558, 262067]; BBSRC
   {[}BB/K01997X/1, BB/I00095X/1, BB/L024225/1]; EMBL; de.NBI project of
   the German Federal Ministry of Education and Research (BMBF) {[}FKZ 031
   A 534A]; Vienna Science and Technology Fund (WWTF) {[}LS11-045];
   Biotechnology and Biological Sciences Research Council {[}BB/L024225/1,
   BB/I000909/1, BB/I00095X/1, BB/K01997X/1, BB/K020145/1] Funding Source:
   researchfish; BBSRC {[}BB/I000909/1, BB/I00095X/1, BB/K01997X/1,
   BB/L024225/1, BB/K020145/1] Funding Source: UKRI},
Funding-Text = {The PRIDE team is or has been recently funded by the Wellcome Trust
   {[}WT085949MA, WT101477MA], the EU FP7 grants `ProteomeXchange'
   {[}260558] and `PRIME-XS' {[}262067], the BBSRC grants `PROCESS'
   {[}BB/K01997X/1], `Quantitative Proteomics' {[}BB/I00095X/1] and
   `ProteoGenomics' {[}BB/L024225/1], and by EMBL core funding. G.M. is
   funded by the de.NBI project of the German Federal Ministry of Education
   and Research (BMBF) {[}FKZ 031 A 534A]. J.G. is funded by a grant of the
   Vienna Science and Technology Fund (WWTF) {[}LS11-045]. Funding for open
   access charge: Wellcome Trust {[}WT101477MA].},
Number-of-Cited-References = {59},
Times-Cited = {2579},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {138},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {DF3QY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000371261700062},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000428127400009,
Author = {Karcher, Sandra and Willighagen, Egon L. and Rumble, John and Ehrhart,
   Friederike and Evelo, Chris T. and Fritts, Martin and Gaheen, Sharon and
   Harper, Stacey L. and Hoover, Mark D. and Jeliazkova, Nina and Lewinski,
   Nastassja and Robinson, Richard L. Marchese and Mills, Karmann C. and
   Mustad, Axel P. and Thomas, Dennis G. and Tsiliki, Georgia and Hendren,
   Christine Ogilvie},
Title = {Integration among databases and data sets to support productive
   nanotechnology: Challenges and recommendations},
Journal = {NANOIMPACT},
Year = {2018},
Volume = {9},
Pages = {85-101},
Month = {JAN},
Abstract = {Many groups within the broad field of nanoinformatics are already
   developing data repositories and analytical tools driven by their
   individual organizational goals. Integrating these data resources across
   disciplines and with non-nanotechnology resources can support multiple
   objectives by enabling the reuse of the same information. Integration
   can also serve as the impetus for novel scientific discoveries by
   providing the framework to support deeper data analyses. This article
   discusses current data integration practices in nanoinformatics and in
   comparable mature fields, and nanotechnology-specific challenges
   impacting data integration. Based on results from a
   nanoinformatics-community-wide survey, recommendations for achieving
   integration of existing operational nanotechnology resources are
   presented. Nanotechnology-specific data integration challenges, if
   effectively resolved, can foster the application and validation of
   nanotechnology within and across disciplines. This paper is one of a
   series of articles by the Nanomaterial Data Curation Initiative that
   address data issues such as data curation workflows, data completeness
   and quality, curator responsibilities, and metadata.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Hendren, CO (Corresponding Author), Duke Univ, CEINT, Box 90287,121 Hudson Hall, Durham, NC 27708 USA.
   Karcher, Sandra, Carnegie Mellon Univ, Civil \& Environm Engn, Pittsburgh, PA 15213 USA.
   Willighagen, Egon L.; Ehrhart, Friederike; Evelo, Chris T., Maastricht Univ, Dept Bioinformat BiGCaT, POB 616,UNS50,Box 19, NL-6200 MD Maastricht, Netherlands.
   Rumble, John, R\&R Data Serv, 11 Montgomery Ave, Gaithersburg, MD 20877 USA.
   Rumble, John, CODATA VAMAS Working Grp Nanomat, Paris, France.
   Fritts, Martin; Gaheen, Sharon, Leidos Biomed Res Inc, Clin Res Directorate, Clin Monitoring Res Program, NCI Campus Frederick, Frederick, MD 21702 USA.
   Harper, Stacey L., Oregon State Univ, Environm \& Mol Toxicol, Corvallis, OR 97331 USA.
   Harper, Stacey L., Oregon State Univ, Sch Chem Biol \& Environm Engn, Corvallis, OR 97331 USA.
   Hoover, Mark D., NIOSH, 1095 Willowdale Rd, Morgantown, WV 26505 USA.
   Jeliazkova, Nina, IdeaConsult Ltd, 4 A Kanchev Str, Sofia 1000, Bulgaria.
   Lewinski, Nastassja, Virginia Commonwealth Univ, Chem \& Life Sci Engn, Richmond, VA 23284 USA.
   Robinson, Richard L. Marchese, Univ Leeds, Sch Chem \& Proc Engn, Leeds LS2 9JT, W Yorkshire, England.
   Robinson, Richard L. Marchese, Liverpool John Moores Univ, Sch Pharm \& Biomol Sci, James Parsons Bldg,Byrom St, Liverpool L3 3AF, Merseyside, England.
   Mills, Karmann C., RTI Int, 3040 Cornwallis Rd, Res Triangle Pk, NC 27709 USA.
   Mustad, Axel P., Nordic Quantum Comp Grp AS, Oslo Sci Pk,POB 1892, N-0124 Oslo, Norway.
   Thomas, Dennis G., Pacific Northwest Natl Lab, Biol Sci Div, Richland, WA USA.
   Tsiliki, Georgia, Natl Tech Univ Athens, Sch Chem Engn, 9 Heroon Polytech St, Athens 15780, Greece.
   Tsiliki, Georgia, ATHENA Res \& Innovat Ctr, Inst Management Informat Syst, Artemidos 6 \& Epidavrou, Athens 15125, Greece.
   Karcher, Sandra; Hendren, Christine Ogilvie, Duke Univ, CEINT, Box 90287,121 Hudson Hall, Durham, NC 27708 USA.},
DOI = {10.1016/j.impact.2017.11.002},
ISSN = {2452-0748},
Keywords = {Nanomaterials; Nanotechnology; Nanoinformatics; Data integration;
   Databases; Web services},
Keywords-Plus = {NANOMATERIAL; INFORMATION; ONTOLOGIES; WEB; DEFINITION; RESOURCES;
   FRAMEWORK; PLATFORM; LINKING; QUALITY},
Research-Areas = {Environmental Sciences \& Ecology; Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Environmental Sciences; Nanoscience \& Nanotechnology},
Author-Email = {christine.hendren@duke.edu},
Affiliations = {Carnegie Mellon University; Maastricht University; National Institutes
   of Health (NIH) - USA; NIH National Cancer Institute (NCI); Frederick
   National Laboratory for Cancer Research; Oregon State University; Oregon
   State University; Centers for Disease Control \& Prevention - USA;
   National Institute for Occupational Safety \& Health (NIOSH); Virginia
   Commonwealth University; University of Leeds; Liverpool John Moores
   University; Research Triangle Institute; United States Department of
   Energy (DOE); Pacific Northwest National Laboratory; National Technical
   University of Athens; Duke University},
ResearcherID-Numbers = {Hendren, Christine Ogilvie/AAM-3502-2021
   Willighagen, Egon/C-6136-2008
   Hoover, Mark D./I-4201-2012
   Jeliazkova, Nina/P-5381-2019
   Evelo, Chris TA/D-2914-2009
   Lewinski, Nastassja/N-1371-2014
   },
ORCID-Numbers = {Hendren, Christine Ogilvie/0000-0002-9546-6545
   Willighagen, Egon/0000-0001-7542-0286
   Hoover, Mark D./0000-0002-8726-8127
   Jeliazkova, Nina/0000-0002-4322-6179
   Evelo, Chris TA/0000-0002-5301-3142
   Ehrhart, Friederike/0000-0002-7770-620X
   Lewinski, Nastassja/0000-0002-9335-9949
   Karcher, Sandra/0000-0003-1206-9817
   Riter, Karmann/0000-0002-3936-4253
   Marchese Robinson, Richard/0000-0001-7648-8645},
Funding-Acknowledgement = {National Science Foundation (NSF); Environmental Protection Agency (EPA)
   under NSF {[}DBI-126625, EF-0830093]; National Institutes of Health
   (NIH) {[}84HHSN268201000022C]; National Cancer Institute, National
   Institutes of Health {[}HHSN261200800001E]; European Union Seventh
   Framework Programme for research, technological development and
   demonstration {[}FP7-NMP-2013-SMALL-7, 604134]; European Union
   {[}FP7-NMP-2012-SMALL-6, 309837]; FutureNanoNeeds project - European
   Union Seventh Framework Programme {[}FP7-NMP-2013-LARGE-7, 604602];
   NanoReg2 project from the European Union's Horizon research and
   innovation programme {[}646221]; NCI Center for Biomedical Informatics
   and Information Technical (CBIIT); NCI Office of Cancer Nanotechnology
   Research (OCNR)},
Funding-Text = {The authors would also like to acknowledge the Nano WG leaders for their
   time and expertise in providing the necessary tools that supported
   collaboration on this article. Authors would like to give special thanks
   to Dr. Mervi Heiskanen, the Nano WG lead from the NCI Center for
   Biomedical Informatics and Information Technical (CBIIT) and Dr.
   Stephanie Morris, from the NCI Office of Cancer Nanotechnology Research
   (OCNR) for their leadership and support for Nano WG initiatives
   including the development of this article and funding of its Open Access
   publication status.; The first three authors are listed in order of
   contributions. The remaining authors, excluding the last, are listed
   alphabetically.; The views, opinions, and content in this article are
   those of the authors and do not necessarily represent the views,
   opinions, or policies of their respective employers or organizations.
   Mention of trade names, commercial products, or organizations does not
   imply endorsement by the U.S. government.; The authors would like to
   gratefully acknowledge several organizations who participated in the
   data integration survey including the:; Center for the Environmental
   Implications of Nano Technology (CEINT) which is funded by the National
   Science Foundation (NSF) and the Environmental Protection Agency (EPA)
   under NSF Cooperative Agreement DBI-126625 and EF-0830093;; Nanomaterial
   Registry, which is funded by the National Institutes of Health (NIH)
   under contract 84HHSN268201000022C;; caNanoLab has been funded in whole
   or in part with federal funds from the National Cancer Institute,
   National Institutes of Health, under Contract No. HHSN261200800001E. The
   content of this publication does not necessarily reflect the views or
   policies of the Department of Health and Human Services, nor does
   mention of trade names, commercial products, or organizations imply
   endorsement by the U.S. Government;; Center for Safety of Substances,
   and Products, National Institute of Public Health and the Environment,
   Netherlands;; DECHEMA; and; eNanoMapper, funded by the European Union
   Seventh Framework Programme for research, technological development and
   demonstration (FP7-NMP-2013-SMALL-7) under grant agreement no. 604134.;
   RLMR is grateful for funding from the European Union Seventh Framework
   Programme (FP7-NMP-2012-SMALL-6) under grant agreement no. 309837
   (NanoPUZZLES project).; JR acknowledges support from the FutureNanoNeeds
   project funded by the European Union Seventh Framework Programme
   (FP7-NMP-2013-LARGE-7) under grant agreement no. 604602.; NJ
   acknowledges support from the NanoReg2 project funded from the European
   Union's Horizon 2020 research and innovation programme under grant
   agreement 646221.},
Number-of-Cited-References = {75},
Times-Cited = {43},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {17},
Journal-ISO = {NanoImpact},
Doc-Delivery-Number = {GA2DQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000428127400009},
OA = {Green Published, Green Accepted, Green Submitted, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000640495900025,
Author = {Bawuah, Prince and Markl, Daniel and Turner, Alice and Evans, Mike and
   Portieri, Alessia and Farrell, Daniel and Lucas, Ralph and Anderson,
   Andrew and Goodwin, Daniel J. and Zeitler, J. Axel},
Title = {A Fast and Non-destructive Terahertz Dissolution Assay for Immediate
   Release Tablets},
Journal = {JOURNAL OF PHARMACEUTICAL SCIENCES},
Year = {2021},
Volume = {110},
Number = {5},
Pages = {2083-2092},
Month = {MAY},
Abstract = {There is a clear need for a robust process analytical technology tool
   that can be used for on-line/in-line prediction of dissolution and
   disintegration characteristics of pharmaceutical tablets during
   manufacture. Tablet porosity is a reliable and fundamental critical
   quality attribute which controls key mass transport mechanisms that
   govern disintegration and dissolution behavior. A measurement protocol
   was developed to measure the total porosity of a large number of tablets
   in transmission without the need for any sample preparation. By using
   this fast and non-destructive terahertz spectroscopy method it is
   possible to predict the disintegration and dissolution of drug from a
   tablet in less than a second per sample without the need of a
   chemometric model. The validity of the terahertz porosity method was
   established across a range of immediate release (IR) formulations of
   ibuprofen and indomethacin tablets of varying geometries as well as with
   and without debossing. Excellent correlation was observed between the
   measured terahertz porosity, dissolution characteristics (time to
   release 50\% drug content) and disintegration time for all samples.
   These promising results and considering the robustness of the terahertz
   method pave the way for a fully automated at-line/on-line porosity
   sensor for real time release testing of IR tablets dissolution. (c) 2021
   American Pharmacists Association (R). Published by Elsevier Inc. All
   rights reserved.},
Publisher = {ELSEVIER SCIENCE INC},
Address = {STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA},
Type = {Article},
Language = {English},
Affiliation = {Zeitler, JA (Corresponding Author), Univ Cambridge, Dept Chem Engn \& Biotechnol, Cambridge, England.
   Bawuah, Prince; Zeitler, J. Axel, Univ Cambridge, Dept Chem Engn \& Biotechnol, Cambridge, England.
   Markl, Daniel; Turner, Alice, Univ Strathclyde, Strathclyde Inst Pharm \& Biomed Sci, Glasgow, Lanark, Scotland.
   Markl, Daniel, Univ Strathclyde, Technol \& Innovat Ctr, EPSRC Future Mfg Res Hub Continuous Mfg \& Adv Cry, Glasgow, Lanark, Scotland.
   Turner, Alice, Univ Strathclyde, Technol \& Innovat Ctr, EPSRC CMAC Future Mfg Res Hub, CMAC Natl Facil, 99 George St, Glasgow G1 1RD, Lanark, Scotland.
   Evans, Mike; Portieri, Alessia; Farrell, Daniel, TeraView Ltd, 1 Enterprise,Cambridge Res Pk, Cambridge CB25 9PD, England.
   Lucas, Ralph, Huxley Bertram Engn Ltd, 53 Pembroke Ave, Cambridge, England.
   Anderson, Andrew; Goodwin, Daniel J., David Jack Ctr, Res \& Dev, GSK, Pk Rd, Ware, Herts, England.},
DOI = {10.1016/j.xphs.2020.11.041},
EarlyAccessDate = {APR 2021},
ISSN = {0022-3549},
EISSN = {1520-6017},
Keywords = {Terahertz spectroscopy; Pharmaceutical tablet; Porosity; disintegration;
   Dissolution; Real time release testing; Process analytical technology},
Keywords-Plus = {PHARMACEUTICAL TABLETS; POROSITY MEASUREMENT; DISINTEGRATION TIME;
   TENSILE-STRENGTH; SPECTROSCOPY; PREDICTION; TRANSMISSION; PROFILES;
   COMPACTS},
Research-Areas = {Pharmacology \& Pharmacy; Chemistry},
Web-of-Science-Categories  = {Chemistry, Medicinal; Chemistry, Multidisciplinary; Pharmacology \&
   Pharmacy},
Author-Email = {jaz22@cam.ac.uk},
Affiliations = {University of Cambridge; University of Strathclyde; UK Research \&
   Innovation (UKRI); Engineering \& Physical Sciences Research Council
   (EPSRC); University of Strathclyde; University of Strathclyde; UK
   Research \& Innovation (UKRI); Engineering \& Physical Sciences Research
   Council (EPSRC); TeraView; GlaxoSmithKline},
ResearcherID-Numbers = {Zeitler, Axel/B-4885-2008
   },
ORCID-Numbers = {Zeitler, Axel/0000-0002-4958-0582
   Turner, Alice Jane/0000-0002-5323-9221
   Markl, Daniel/0000-0003-0411-733X},
Funding-Acknowledgement = {Innovate UK {[}104196]; EPSRC {[}EP/P006965/1] Funding Source: UKRI;
   Innovate UK {[}104196] Funding Source: UKRI},
Funding-Text = {The research received financial support from Innovate UK (ref: 104196).
   The raw data that was used to prepare the figures in this manuscript can
   be downloaded from the University of Cambridge Open Data Repository at
   https://doi.org/10.17863/CAM.62356.},
Number-of-Cited-References = {51},
Times-Cited = {13},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {10},
Journal-ISO = {J. Pharm. Sci.},
Doc-Delivery-Number = {RN6XW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000640495900025},
OA = {Green Submitted, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000525956700075,
Author = {Wu, Sicheng and Sun, Chuqing and Li, Yanze and Wang, Teng and Jia,
   Longhao and Lai, Senying and Yang, Yaling and Luo, Pengyu and Dai, Die
   and Yang, Yong-Qing and Luo, Qibin and Gao, Na L. and Ning, Kang and He,
   Li-jie and Zhao, Xing-Ming and Chen, Wei-Hua},
Title = {GMrepo: a database of curated and consistently annotated human gut
   metagenomes},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2020},
Volume = {48},
Number = {D1},
Pages = {D545-D553},
Month = {JAN 8},
Abstract = {GMrepo (data repository for Gut Microbiota) is a database of curated and
   consistently annotated human gut metagenomes. Its main purpose is to
   facilitate the reusability and accessibility of the rapidly growing
   human metagenomic data. This is achieved by consistently annotating the
   microbial contents of collected samples using state-of-art toolsets and
   by manual curation of the meta-data of the corresponding human hosts.
   GMrepo organizes the collected samples according to their associated
   phenotypes and includes all possible related meta-data such as age, sex,
   country, body-mass-index (BMI) and recent antibiotics usage. To make
   relevant information easier to access, GMrepo is equipped with a
   graphical query builder, enabling users to make customized, complex and
   biologically relevant queries. For example, to find (1) samples from
   healthy individuals of 18 to 25 years old with BMIs between 18.5 and
   24.9, or (2) projects that are related to colorectal neoplasms, with
   each containing>100 samples and both patients and healthy controls.
   Precomputed species/genus relative abundances, prevalence within and
   across phenotypes, and pairwise co-occurrence information are all
   available at the website and accessible through programmable interfaces.
   So far, GMrepo contains 58 903 human gut samples/runs (including 17 618
   metagenomes and 41 285 amplicons) from 253 projects concerning 92
   phenotypes. GMrepo is freely available at: https://gmrepo.humangut.info.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Chen, WH (Corresponding Author), Huazhong Univ Sci \& Technol, Coll Life Sci \& Technol, Dept Bioinformat \& Syst Biol, Key Lab Mol Biophys,Minist Educ,Hubei Key Lab Bio, Wuhan 430074, Hubei, Peoples R China.
   Chen, WH (Corresponding Author), Huazhong Univ Sci \& Technol, Ezhou Ind Technol Res Inst, Ezhou 436044, Hubei, Peoples R China.
   He, LJ (Corresponding Author), Peoples Hosp Liaoning Prov, Dept Med Oncol, Shenyang 110016, Peoples R China.
   Zhao, XM (Corresponding Author), Fudan Univ, Inst Sci \& Technol Brain Inspired Intelligence, Shanghai 200433, Peoples R China.
   Zhao, XM (Corresponding Author), Minist Educ, Key Lab Computat Neurosci \& Brain Inspired Intell, Shanghai, Peoples R China.
   Chen, WH (Corresponding Author), HeNan Normal Univ, Coll Life Sci, Xinxiang 453007, Henan, Peoples R China.
   Wu, Sicheng; Sun, Chuqing; Li, Yanze; Wang, Teng; Jia, Longhao; Lai, Senying; Yang, Yaling; Luo, Pengyu; Dai, Die; Gao, Na L.; Ning, Kang; Chen, Wei-Hua, Huazhong Univ Sci \& Technol, Coll Life Sci \& Technol, Dept Bioinformat \& Syst Biol, Key Lab Mol Biophys,Minist Educ,Hubei Key Lab Bio, Wuhan 430074, Hubei, Peoples R China.
   Yang, Yaling, Shenzhen Digital Life Inst, Shenzhen 518053, Guangdong, Peoples R China.
   Yang, Yong-Qing, Huazhong Univ Sci \& Technol, Sch Phys, Wuhan 430070, Hubei, Peoples R China.
   Luo, Qibin, Tech Univ Munich, Dept Genome Oriented Bioinformat, Wissenschaftszentrum Weihenstephan, D-85350 Freising Weihenstephan, Germany.
   Gao, Na L., Heinrich Heine Univ, Inst Comp Sci \& Dept Biol, D-40225 Dusseldorf, Germany.
   Ning, Kang; Chen, Wei-Hua, Huazhong Univ Sci \& Technol, Ezhou Ind Technol Res Inst, Ezhou 436044, Hubei, Peoples R China.
   He, Li-jie, Peoples Hosp Liaoning Prov, Dept Med Oncol, Shenyang 110016, Peoples R China.
   Zhao, Xing-Ming, Fudan Univ, Inst Sci \& Technol Brain Inspired Intelligence, Shanghai 200433, Peoples R China.
   Zhao, Xing-Ming, Minist Educ, Key Lab Computat Neurosci \& Brain Inspired Intell, Shanghai, Peoples R China.
   Chen, Wei-Hua, HeNan Normal Univ, Coll Life Sci, Xinxiang 453007, Henan, Peoples R China.},
DOI = {10.1093/nar/gkz764},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MICROBIOME; CANCER},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {17702488896@163.com
   xmzhao@fudan.edu.cn
   weihuachen@hust.edu.cn},
Affiliations = {Huazhong University of Science \& Technology; Huazhong University of
   Science \& Technology; Technical University of Munich; Heinrich Heine
   University Dusseldorf; Huazhong University of Science \& Technology;
   Fudan University; Henan Normal University},
ResearcherID-Numbers = {Luo, pengyu/JDD-4531-2023
   Ning, Kang/ABD-3446-2020
   li, yanze/JHT-4361-2023
   Chen, Weihua/GRS-9256-2022
   },
ORCID-Numbers = {Luo, pengyu/0009-0006-0069-4067
   Ning, Kang/0000-0003-3325-5387
   Chen, Wei-Hua/0000-0003-2168-6147
   Sun, Chuqing/0000-0001-5025-2650
   Li, Yanze/0000-0002-8771-7279
   , delicia/0000-0001-5309-8046},
Funding-Acknowledgement = {National Key Research and Development Program of China
   {[}2018YFC0910502]; National Key R\&D Program of China
   {[}2018YFC0910500]; National Natural Science Foundation of China
   {[}61932008, 61772368, 61572363]; Natural Science Foundation of Shanghai
   {[}17ZR1445600]; ShanghaiMunicipal Science and Technology Major Project
   {[}2018SHZDZX01]; ZJLab},
Funding-Text = {Funding for open access charge: National Key Research and Development
   Program of China {[}2018YFC0910502 to W.H.C.]. This work was partly
   supported by National Key R\&D Program of China (2018YFC0910500),
   National Natural Science Foundation of China (61932008, 61772368,
   61572363), Natural Science Foundation of Shanghai (17ZR1445600),
   ShanghaiMunicipal Science and Technology Major Project (2018SHZDZX01)
   and ZJLab.},
Number-of-Cited-References = {41},
Times-Cited = {73},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {50},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {LD3UB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000525956700075},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000389570100106,
Author = {Anderson, Carrie L. and Becher, Heiko and Winkler, Volker},
Title = {Tobacco Control Progress in Low and Middle Income Countries in
   Comparison to High Income Countries},
Journal = {INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH},
Year = {2016},
Volume = {13},
Number = {10},
Month = {OCT},
Abstract = {The study aimed to describe worldwide levels and trends of tobacco
   control policy by comparing low and middle income countries with other
   income categories from 2007 to 2014 and to analyze the corresponding
   relation to recent changes in smoking prevalence. Policy measure data
   representing years 2007 to 2014 were collected from all available World
   Health Organization (WHO) reports on the global tobacco epidemic.
   Corresponding policy percentage scores (PS) were calculated based on
   MPOWER measures. Age-standardized smoking prevalence data for years 2010
   and 2015 were collected from the WHO Global Health Observatory Data
   Repository. Trends of PS were analysed with respect to WHO region and
   OECD country income category. Scatter plots and regression analysis were
   used to depict the relationship between tobacco control policy of 2010
   and change in smoking prevalence between 2015 and 2010 by sex and income
   category. Combined PS for all countries increased significantly from
   47\% in 2007 to 61\% by 2014 (p < 0.001). When grouped by income
   category and region, policies were strengthened in all categories,
   albeit with varying progression. By 2014, tobacco control policy
   legislation had reached 45\% in the Least Developed Countries (LDCs),
   59\% in Low Middle Income Countries (LMICs), 66\% in Upper Middle Income
   Countries (UMICs) and 70\% in High Income Countries (HICs). Overall,
   there was a negative relationship between higher policy scores and
   change in smoking prevalence. Although policy strengthening had been
   conducted between 2007 and 2014, room for considerable global
   improvement remains, particularly in LDCs.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Winkler, V (Corresponding Author), Heidelberg Univ, Inst Publ Hlth, D-69120 Heidelberg, Germany.
   Anderson, Carrie L., Charite, Inst Trop Med \& Int Hlth, D-13353 Berlin, Germany.
   Becher, Heiko, Univ Med Ctr Hamburg Eppendorf, Inst Med Biometry \& Epidemiol, D-20246 Hamburg, Germany.
   Winkler, Volker, Heidelberg Univ, Inst Publ Hlth, D-69120 Heidelberg, Germany.},
DOI = {10.3390/ijerph13101039},
Article-Number = {1039},
EISSN = {1660-4601},
Keywords = {smoking prevalence; policy measures; tobacco control; MPOWER; global
   tobacco epidemic; low income countries; middle income countries},
Keywords-Plus = {CONTROL POLICIES; ARTICLES; IMPACT},
Research-Areas = {Environmental Sciences \& Ecology; Public, Environmental \& Occupational
   Health},
Web-of-Science-Categories  = {Environmental Sciences; Public, Environmental \& Occupational Health},
Author-Email = {carrie.l.anderson@gmail.com
   h.becher@uke.de
   v.winkler@uni-heidelberg.de},
Affiliations = {Free University of Berlin; Humboldt University of Berlin; Charite
   Universitatsmedizin Berlin; University of Hamburg; University Medical
   Center Hamburg-Eppendorf; Ruprecht Karls University Heidelberg},
ResearcherID-Numbers = {Winkler, Volker Franz/GYV-4278-2022
   Becher, Heiko/ABI-1234-2020
   },
ORCID-Numbers = {Winkler, Volker Franz/0000-0002-9974-1145
   Becher, Heiko/0000-0002-8808-6667},
Funding-Acknowledgement = {Deutsche Forschungsgemeinschaft; Ruprecht-Karls-Universitat Heidelberg},
Funding-Text = {This manuscript was written to fulfill requirements for the thesis
   component of the MScIH program at Charite-Universitatsmedizin Berlin.
   Matthias Borchert is thanked for critical input. We acknowledge the
   financial support of the Deutsche Forschungsgemeinschaft and
   Ruprecht-Karls-Universitat Heidelberg within the funding programme Open
   Access Publishing.},
Number-of-Cited-References = {32},
Times-Cited = {55},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Int. J. Environ. Res. Public Health},
Doc-Delivery-Number = {EE4KF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000389570100106},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000727758000001,
Author = {Stefen, Clara and Wagner, Franziska and Asztalos, Marika and Giere,
   Peter and Grobe, Peter and Hiller, Michael and Hofmann, Rebecca and
   Jaehde, Maria and Laechele, Ulla and Lehmann, Thomas and Ortmann, Sylvia
   and Peters, Benjamin and Ruf, Irina and Schiffmann, Christian and Thier,
   Nadja and Unterhitzenberger, Gabriele and Vogt, Lars and Rudolf,
   Matthias and Wehner, Peggy and Stuckas, Heiko},
Title = {Phenotyping in the era of genomics: <i>MaTrics</i>-a digital character
   matrix to document mammalian phenotypic traits},
Journal = {MAMMALIAN BIOLOGY},
Year = {2022},
Volume = {102},
Number = {1},
Pages = {235-249},
Month = {FEB},
Abstract = {A new and uniquely structured matrix of mammalian phenotypes, MaTrics
   (Mammalian Tains for Comparative Genomics) in a digital form is
   presented. By focussing on mammalian species for which genome assemblies
   are available, MaTrics provides an interface between mammalogy and
   comparative genomics.
   MaTrics was developed within a project aimed to find genetic causes of
   phenotypic traits of mammals using Forward Genomics. This approach
   requires genomes and comprehensive and recorded information on
   homologous phenotypes that are coded as discrete categories in a matrix.
   MaTrics is an evolving online resource providing information on
   phenotypic traits in numeric code; traits are coded either as
   absent/present or with several states as multistate. The state record
   for each species is linked to at least one reference (e.g., literature,
   photographs, histological sections, CT scans, or museum specimens) and
   so MaTrics contributes to digitalization of museum collections.
   Currently, MaTrics covers 147 mammalian species and includes 231
   characters related to structure, morphology, physiology, ecology, and
   ethology and available in a machine actionable NEXUS-format{*}. Filling
   MaTrics revealed substantial knowledge gaps, highlighting the need for
   phenotyping efforts. Studies based on selected data from MaTrics and
   using Forward Genomics identified associations between genes and certain
   phenotypes ranging from lifestyles (e.g., aquatic) to dietary
   specializations (e.g., herbivory, carnivory). These findings motivate
   the expansion of phenotyping in MaTrics by filling research gaps and by
   adding taxa and traits. Only databases like MaTrics will provide machine
   actionable information on phenotypic traits, an important limitation to
   genomics. MaTrics is available within the data repository Morph.D.Base
   (www.morphdbase.de).},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Stefen, C (Corresponding Author), Senckenberg Naturhistor Sammlungen Dresden, Konigsbrucker Landstr 159, D-01109 Dresden, Germany.
   Stefen, Clara; Wagner, Franziska; Asztalos, Marika; Jaehde, Maria; Peters, Benjamin; Thier, Nadja; Stuckas, Heiko, Senckenberg Naturhistor Sammlungen Dresden, Konigsbrucker Landstr 159, D-01109 Dresden, Germany.
   Giere, Peter; Laechele, Ulla, Leibniz Inst Evolut \& Biodivers Sci, Museum Naturkunde, Invalidenstr 43, D-10115 Berlin, Germany.
   Grobe, Peter, Zool Forschungsmuseum Alexander Koenig, Adenauerallee 160, D-53113 Bonn, Germany.
   Hiller, Michael, Max Planck Inst Mol Cell Biol \& Genet, Pfotenhauerstr 108, D-01307 Dresden, Germany.
   Hiller, Michael, Max Planck Inst Phys Komplexer Syst, Nothnitzer Str 38, D-01187 Dresden, Germany.
   Hiller, Michael, Ctr Syst Biol Dresden, Pfotenhauerstr 108, D-01307 Dresden, Germany.
   Hiller, Michael, LOEWE Ctr Translat Biodivers Genom, Senckenberganlage 25, D-60325 Frankfurt, Germany.
   Hiller, Michael; Hofmann, Rebecca; Lehmann, Thomas; Ruf, Irina, Senckenberg Forschungsinstitut \& Naturmuseum, Abt Messelforschung \& Mammal, Senckenberganlage 25, D-60325 Frankfurt, Germany.
   Hiller, Michael, Goethe Univ, Fac Biosci, Max von Laue Str 9, D-60438 Frankfurt, Germany.
   Hofmann, Rebecca; Ruf, Irina, Goethe Univ, Inst Geowissensch, Altenhoferallee 1, D-60438 Frankfurt, Germany.
   Laechele, Ulla, Humboldt Univ, Inst Biol, Invalidenstr 42, D-10115 Berlin, Germany.
   Ortmann, Sylvia; Schiffmann, Christian; Unterhitzenberger, Gabriele, Leibniz Inst Zoo \& Wildlife Res, Alfred Kowalke Str 17, D-10315 Berlin, Germany.
   Vogt, Lars, TIB Leibniz Informat Ctr Sci \& Technol, Welfengarten 1B, D-30167 Hannover, Germany.
   Rudolf, Matthias; Wehner, Peggy, Tech Univ Dresden, Inst Allgemeine Psychol, Biopsychol \& Methoden Psychol, Raum BZW A317, D-01062 Dresden, Germany.},
DOI = {10.1007/s42991-021-00192-5},
EarlyAccessDate = {DEC 2021},
ISSN = {1616-5047},
EISSN = {1618-1476},
Keywords = {Comparative genomics; Discrete character states; Hard tissue; Museum
   specimens; Numeric coding; Visceral \& life history traits},
Keywords-Plus = {MODEL ORGANISM; LOGICAL BASIS; GENERATION; ZEBRAFISH; EVOLUTION;
   HOMOLOGY; PLATFORM; BIOLOGY; FOXI3; GENE},
Research-Areas = {Zoology},
Web-of-Science-Categories  = {Zoology},
Author-Email = {clara.stefen@senckenberg.de},
Affiliations = {Senckenberg Gesellschaft fur Naturforschung (SGN); Leibniz Institut fur
   Evolutions und Biodiversitatsforschung; Zoologisches Forschungsmuseum
   Alexander Koenig (ZFMK); Max Planck Society; Max Planck Society;
   Senckenberg Gesellschaft fur Naturforschung (SGN); Goethe University
   Frankfurt; Goethe University Frankfurt; Humboldt University of Berlin;
   Leibniz Institut fur Zoo und Wildtierforschung; Technische Universitat
   Dresden},
ResearcherID-Numbers = {Vogt, Lars/K-4166-2012
   Stuckas, Heiko/AFM-0009-2022
   Ortmann, Sylvia/B-7088-2015
   },
ORCID-Numbers = {Vogt, Lars/0000-0002-8280-0487
   Stuckas, Heiko/0000-0002-5690-0994
   Ortmann, Sylvia/0000-0003-2520-6251
   Hofmann, Rebecca/0000-0003-4985-6099
   Hiller, Michael/0000-0003-3024-1449
   Asztalos, Marika/0000-0002-4090-1159
   Wehner, Peggy/0000-0001-9149-8614
   Lehmann, Thomas/0000-0002-1946-7968
   W, F/0000-0001-6623-6700
   Giere, Peter/0000-0002-5570-0085},
Funding-Acknowledgement = {Leibnitz Association {[}SAW-2016-SGN-2]},
Funding-Text = {Open Access funding enabled and organized by Projekt DEAL. This work was
   funded as part of the interdisciplinary research project `Identifying
   genomic loci underlying mammalian phenotypic variability using Forward
   Genomics' by the Leibnitz Association, grant SAW-2016-SGN-2.},
Number-of-Cited-References = {83},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Mamm. Biol.},
Doc-Delivery-Number = {ZH5FY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000727758000001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000626723800033,
Author = {Casas-Pastor, Delia and Mueller, Raphael Rene and Jaenicke, Sebastian
   and Brinkrolf, Karina and Becker, Anke and Buttner, Mark and Gross,
   Carol and Mascher, Thorsten and Goesmann, Alexander and Fritz, Georg},
Title = {Expansion and re-classification of the extracytoplasmic function (ECF) σ
   factor family},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2021},
Volume = {49},
Number = {2},
Month = {JAN 25},
Abstract = {Extracytoplasmic function sigma factors (ECFs) represent one of the
   major bacterial signal transduction mechanisms in terms of abundance,
   diversity and importance, particularly in mediating stress responses.
   Here, we performed a comprehensive phylogenetic analysis of this protein
   family by scrutinizing all proteins in the NCBI database. As a result,
   we identified an average of similar to 10 ECFs per bacterial genome and
   157 phylogenetic ECF groups that feature a conserved genetic
   neighborhood and a similar regulation mechanism. Our analysis expands
   previous classification efforts similar to 50-fold, enriches many
   original ECF groups with previously unclassified proteins and identifies
   22 entirely new ECF groups. The ECF groups are hierarchically related to
   each other and are further composed of subgroups with closely related
   sequences. This two-tiered classification allows for the accurate
   prediction of common promoter motifs and the inference of putative
   regulatory mechanisms across subgroups composing an ECF group. This
   comprehensive, high-resolution description of the phylogenetic
   distribution of the ECF family, together with the massive expansion of
   classified ECF sequences and an openly accessible data repository called
   `ECF Hub' (https://www.computational , bio.uni-giessen.de/ecfhub), will
   serve as a powerful hypothesis-generator to guide future research in the
   field.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Fritz, G (Corresponding Author), Univ Western Australia, Sch Mol Sci, Perth, WA 6009, Australia.
   Casas-Pastor, Delia; Becker, Anke, Philipps Univ Marburg, Ctr Synthet Microbiol SYNMIKRO, Marburg, Germany.
   Mueller, Raphael Rene; Jaenicke, Sebastian; Brinkrolf, Karina; Goesmann, Alexander, Justus Liebig Univ, Bioinformat \& Syst Biol, Giessen, Germany.
   Buttner, Mark, John Innes Ctr, Dept Mol Microbiol, Norwich Res Pk, Norwich NR4 7UH, Norfolk, England.
   Gross, Carol, Univ Calif San Francisco, Dept Microbiol \& Immunol, San Francisco, CA 94158 USA.
   Gross, Carol, Univ Calif San Francisco, Dept Cell \& Tissue Biol, San Francisco, CA 94158 USA.
   Mascher, Thorsten, Tech Univ Dresden, Inst Microbiol, Dresden, Germany.
   Fritz, Georg, Univ Western Australia, Sch Mol Sci, Perth, WA 6009, Australia.},
DOI = {10.1093/nar/gkaa1229},
EarlyAccessDate = {JAN 2021},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {STRUCTURAL BASIS; SIGNAL-TRANSDUCTION; OXIDATIVE STRESS;
   GENE-EXPRESSION; WEB SERVER; TRANSCRIPTION; RECOGNITION; PREDICTION;
   PROTEINS; TOPOLOGY},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {georg.fritz@uwa.edu.au},
Affiliations = {Philipps University Marburg; Justus Liebig University Giessen; UK
   Research \& Innovation (UKRI); Biotechnology and Biological Sciences
   Research Council (BBSRC); John Innes Center; University of California
   System; University of California San Francisco; University of California
   System; University of California San Francisco; Technische Universitat
   Dresden; University of Western Australia},
ResearcherID-Numbers = {Fritz, Georg/F-3910-2010
   },
ORCID-Numbers = {Fritz, Georg/0000-0002-1503-9165
   Buttner, Mark/0000-0002-3505-2981
   Mascher, Thorsten/0000-0002-6300-5541
   Muller, Raphael Rene/0000-0003-2594-4131
   Becker, Anke/0000-0003-4561-9184},
Funding-Acknowledgement = {German Federal Ministry of Education and Research (BMBF); Biotechnology
   and Biological Sciences Research Council (BBSRC) via the joint ERASynBio
   project ECF-express {[}BMBF] {[}031L0010B, 031L0010A]; Biotechnology and
   Biological Sciences Research Council (BBSRC) via the joint ERASynBio
   project ECF-express {[}BBSRC] {[}BB/N006852/1]; BBSRC Institute
   Strategic Programme Grant {[}BB/J004561/1]; project `Bielefeld-Giessen
   Center for Microbial BioinformaticsBiGi' within the German Network for
   Bioinformatics Infrastructure (de.NBI) {[}031A533]; University of
   Western Australia; BBSRC {[}BB/N006852/1, BBS/E/J/000PR9791,
   BB/L019825/1, BB/I00873X/1] Funding Source: UKRI},
Funding-Text = {German Federal Ministry of Education and Research (BMBF); Biotechnology
   and Biological Sciences Research Council (BBSRC) via the joint ERASynBio
   project ECF-express {[}BMBF grant 031L0010B to A.B., A.G., G.F.,
   031L0010A to T.M., BBSRC grant BB/N006852/1 to M.J.B.]; BBSRC Institute
   Strategic Programme Grant {[}BB/J004561/1 to the John Innes Centre];
   project `Bielefeld-Gie ss en Center for Microbial BioinformaticsBiGi'
   {[}031A533 to R.R.M., S.J., K.B.] within the German Network for
   Bioinformatics Infrastructure (de.NBI). Funding for open access charge:
   The University of Western Australia.},
Number-of-Cited-References = {60},
Times-Cited = {25},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {QT6UH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000626723800033},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000679752200001,
Author = {Truong, Chi T. L. and Le, Hoa V. and Kamauu, Aaron W. and Holmen, John
   R. and Fillmore, Christopher L. and Kobayashi, Monica G. and Wong,
   Schiffon L.},
Title = {Creating a Real-World Data, United States Healthcare Claims-Based
   Adaptation of Kurtzke Functional Systems Scores for Assessing Multiple
   Sclerosis Severity and Progression},
Journal = {ADVANCES IN THERAPY},
Year = {2021},
Volume = {38},
Number = {9},
Pages = {4786-4797},
Month = {SEP},
Abstract = {Introduction This article describes the development of a unique mapping
   of the Kurtzke Functional Systems Scores (KFSS) from International
   Classification of Diseases, 9th revision, Clinical Modification
   (ICD-9-CM) codes among multiple sclerosis (MS) patients within a US
   Integrated Delivery Network (IDN). Valid identification of increasing
   disability may allow deeper insight into MS progression and possible
   treatments. Methods This cohort study identified MS patients in the IDN,
   Intermountain Healthcare. Experienced clinicians and informaticists
   mapped electronic health record ICD-9-CM codes to KFSS components
   generating a modified Kurtzke Expanded Disability Status Scale (EDSS).
   Modified EDSS scores were used to assess disability progression by
   calculating means, medians, ranges, and changes in KFSS and modified
   EDSS scores. Results Overall, 608/2960 (20.5\%) patients were identified
   as having MS progression and presented a wide range of scores on the
   EDSS 10-point scale. The median (range) first and second EDSS scores
   were 0 (0-6) and 5 (1-8), respectively. The median (range) change from
   first to second score was 5 (1-7.5). The median first KFSS score for all
   systems was 0, and the mean differed among components. The highest mean
   first KFSS score (1.06) was measured for sensory function and lowest
   (0.12) for cerebellar functions. Of the 544 patients with their first
   EDSS scores in the <= 2.5 group, 75.2\% and 15.1\% had their second EDSS
   scores in group 3-5.5 and >= 6, respectively. Of the 62 patients with
   their first EDSS score in the 3-5.5 group, 58.1\% had their second EDSS
   scores in group >= 6. Conclusion This innovative mapping technique is a
   promising method for future comparative effectiveness and safety
   research of Disease-Modifying Therapy in Real-World Data repositories.
   Future research to validate and expand on this method in another
   healthcare database is encouraged.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Le, HV (Corresponding Author), PAREXEL Int, 2520 Meridian Pkwy 200, Durham, NC 27713 USA.
   Truong, Chi T. L., MedCodeWorld, Chapel Hill, NC USA.
   Le, Hoa V., PAREXEL Int, 2520 Meridian Pkwy 200, Durham, NC 27713 USA.
   Kamauu, Aaron W., PAREXEL, Bountiful, UT USA.
   Holmen, John R.; Fillmore, Christopher L., Intermt Healthcare, Murray, UT USA.
   Kobayashi, Monica G., PAREXEL, Durham, NC USA.
   Wong, Schiffon L., EMD Serono, Billerica, MA USA.},
DOI = {10.1007/s12325-021-01858-9},
EarlyAccessDate = {JUL 2021},
ISSN = {0741-238X},
EISSN = {1865-8652},
Keywords = {ICD-9 mapping; KFSS; EDSS; MS disability; Algorithm; Real-world data},
Keywords-Plus = {DISABILITY; IMPAIRMENT; SCALE; EDSS},
Research-Areas = {Research \& Experimental Medicine; Pharmacology \& Pharmacy},
Web-of-Science-Categories  = {Medicine, Research \& Experimental; Pharmacology \& Pharmacy},
Author-Email = {hoa.vanle@gmail.com},
Affiliations = {Parexel International; Intermountain Healthcare; Intermountain Medical
   Center},
Funding-Acknowledgement = {EMD Serono; healthcare business of Merck KGaA, Darmstadt, Germany},
Funding-Text = {This study was funded by EMD Serono (CrossRef Funder ID:
   https://doi.org/10.13039/100004755).The Advances in Therapy Rapid
   Service and Open Access fees have been funded by the healthcare business
   of Merck KGaA, Darmstadt, Germany (CrossRef Funder ID:
   https://doi.org/10.13039/100009945).},
Number-of-Cited-References = {24},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Adv. Ther.},
Doc-Delivery-Number = {UL1FA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000679752200001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000743496700066,
Author = {Perez-Riverol, Yasset and Bai, Jingwen and Bandla, Chakradhar and
   Garcia-Seisdedos, David and Hewapathirana, Suresh and Kamatchinathan,
   Selvakumar and Kundu, Deepti J. and Prakash, Ananth and Frericks-Zipper,
   Anika and Eisenacher, Martin and Walzer, Mathias and Wang, Shengbo and
   Brazma, Alvis and Vizcaino, Juan Antonio},
Title = {The PRIDE database resources in 2022: a hub for mass spectrometry-based
   proteomics evidences},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2022},
Volume = {50},
Number = {D1},
Pages = {D543-D552},
Month = {JAN 7},
Abstract = {The PRoteomics IDEntifications (PRIDE) database
   (https://www.ebi.ac.uk/pride/) is the world's largest data repository of
   mass spectrometry-based proteomics data. PRIDE is one of the founding
   members of the global ProteomeXchange (PX) consortium and an ELIXIR core
   data resource. In this manuscript, we summarize the developments in
   PRIDE resources and related tools since the previous update manuscript
   was published in Nucleic Acids Research in 2019. The number of submitted
   datasets to PRIDE Archive (the archival component of PRIDE) has reached
   on average around 500 datasets per month during 2021. In addition to
   continuous improvements in PRIDE Archive data pipelines and
   infrastructure, the PRIDE Spectra Archive has been developed to provide
   direct access to the submitted mass spectra using Universal Spectrum
   Identifiers. As a key point, the file format MAGE-TAB for proteomics has
   been developed to enable the improvement of sample metadata annotation.
   Additionally, the resource PRIDE Peptidome provides access to aggregated
   peptide/protein evidences across PRIDE Archive. Furthermore, we will
   describe how PRIDE has increased its efforts to reuse and disseminate
   high-quality proteomics data into other added-value resources such as
   UniProt, Ensembl and Expression Atlas.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Perez-Riverol, Y; Vizcaíno, JA (Corresponding Author), European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Perez-Riverol, Yasset; Bai, Jingwen; Bandla, Chakradhar; Garcia-Seisdedos, David; Hewapathirana, Suresh; Kamatchinathan, Selvakumar; Kundu, Deepti J.; Prakash, Ananth; Walzer, Mathias; Wang, Shengbo; Brazma, Alvis; Vizcaino, Juan Antonio, European Bioinformat Inst EMBL EBI, European Mol Biol Lab, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Frericks-Zipper, Anika; Eisenacher, Martin, Ruhr Univ Bochum, Med Fac, Med Proteom Ctr, D-44801 Bochum, Germany.
   Frericks-Zipper, Anika; Eisenacher, Martin, Ruhr Univ Bochum, Ctr Prot Diagnost PRODI, Med Proteome Anal, D-44801 Bochum, Germany.},
DOI = {10.1093/nar/gkab1038},
EarlyAccessDate = {NOV 2021},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PROTEIN IDENTIFICATION; CLINICAL PROTEOMICS; JAVA INTERFACE; STANDARD;
   PROTEOMEXCHANGE; BIOINFORMATICS; VISUALIZATION; PEPTIDEATLAS; NEED; API},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {yperez@ebi.ac.uk
   juan@ebi.ac.uk},
Affiliations = {Wellcome Trust Sanger Institute; European Molecular Biology Laboratory
   (EMBL); Ruhr University Bochum; Ruhr University Bochum},
ResearcherID-Numbers = {Bai, Jingwen/AAG-3794-2019
   Perez-Riverol, Yasset/H-2873-2019
   Vizcaino, Juan Antonio/C-3691-2009
   Eisenacher, Martin/J-8044-2014
   },
ORCID-Numbers = {Perez-Riverol, Yasset/0000-0001-6579-6941
   Vizcaino, Juan Antonio/0000-0002-3905-4335
   Eisenacher, Martin/0000-0003-2687-7444
   Walzer, Mathias/0000-0003-4538-2754
   Prakash, Ananth/0000-0001-5799-9618
   Brazma, Alvis/0000-0001-5988-7409
   Wang, Shengbo/0000-0001-5034-6374
   Hewapathirana, Suresh/0000-0002-7862-5022},
Funding-Acknowledgement = {Wellcome {[}208391/Z/17/Z]; BBSRC grant `Proteomics DIA'
   {[}BB/P024599/1]; BBSRC grant `PTMeXchange' {[}BB/S01781X/1]; BBSRC
   grant `GRAPPA' {[}BB/T019670/1]; UK-Japan Partnership award
   {[}BB/N022440/1]; NIH `Proteomics Standards' grant {[}R24 GM127667-01];
   EU H2020 project EPIC-XS {[}823839]; Luxembourg National Research Fund
   {[}C19/BM/13684739]; EMBL; German Federal Ministry of Education and
   Research (BMBF) {[}FKZ 031 A 534A]; Center for Protein Diagnostics
   (PPRODI); Ministry of Innovation, Science and Research of North-Rhine
   Westphalia, Germany;  {[}OTAR-043]; BBSRC {[}BB/T019670/1, BB/S01781X/1,
   BB/P024599/1] Funding Source: UKRI; Wellcome Trust {[}208391/Z/17/Z]
   Funding Source: Wellcome Trust},
Funding-Text = {Wellcome {[}208391/Z/17/Z]; BBSRC grants `Proteomics DIA'
   {[}BB/P024599/1], `PTMeXchange' {[}BB/S01781X/1], `GRAPPA'
   {[}BB/T019670/1]; UK-Japan Partnership award {[}BB/N022440/1]; NIH
   `Proteomics Standards' grant {[}R24 GM127667-01]; EU H2020 project
   EPIC-XS {[}823839]; Open Targets {[}OTAR-043]; Luxembourg National
   Research Fund {[}C19/BM/13684739]; several ELIXIR Implementation Studies
   and EMBL core funding; M.E. and A.F.-Z. would like to acknowledge
   funding from de.NBI, a project of the German Federal Ministry of
   Education and Research (BMBF) {[}FKZ 031 A 534A]; Center for Protein
   Diagnostics (PPRODI), a grant of the Ministry of Innovation, Science and
   Research of North-Rhine Westphalia, Germany. Funding for open access
   charge: Wellcome. Conflict of interest statement. None declared.},
Number-of-Cited-References = {58},
Times-Cited = {1699},
Usage-Count-Last-180-days = {33},
Usage-Count-Since-2013 = {99},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {YH9RO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000743496700066},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000886238300001,
Author = {Price-Jones, Veronica and Brown, Peter M. J. and Adriaens, Tim and
   Tricarico, Elena and Farrow, Rachel A. and Cardoso, Ana Cristina and
   Gervasini, Eugenio and Groom, Quentin and Reyserhove, Lien and Schade,
   Sven and Tsinaraki, Chrisa and Marchante, Elizabete},
Title = {Eyes on the aliens: citizen science contributes to research, policy and
   management of biological invasions in Europe},
Journal = {NEOBIOTA},
Year = {2022},
Volume = {78},
Pages = {1-24},
Month = {NOV 11},
Abstract = {Invasive alien species (IAS) are a key driver of global biodiversity
   loss. Reducing their spread and impact is a target of the Sustainable
   Development Goals (SDG target 15.8) and of the EU IAS Regulation
   1143/2014. The use of citizen science offers various benefits to alien
   species' decision-making and to so-ciety, since public participation in
   research and management boosts awareness, engagement and scientific
   literacy and can reduce conflict in IAS management. We report the
   results of a survey on alien species citizen science initiatives within
   the framework of the European Cooperation in Science and Technology
   (COST) Action Alien-CSI. We gathered metadata on 103 initiatives across
   41 countries, excluding gen-eral biodiversity reporting portals,
   spanning from 2005 to 2020, offering the most comprehensive account of
   alien species citizen science initiatives on the continent to date. We
   retrieved information on project scope, policy relevance, engagement
   methods, data capture, data quality and data management, methods and
   technologies applied and performance indicators such as the number of
   records coming from projects, the numbers of participants and
   publications. The 103 initiatives were unevenly distributed
   geographical-ly, with countries with a tradition of citizen science
   showing more active projects. The majority of projects were contributory
   and were run at a national scale, targeting the general public, alien
   plants and insects, and terrestrial ecosystems. These factors of project
   scope were consistent between geographic regions. Most projects focused
   on collecting species presence or abundance data, aiming to map presence
   and spread. As 75\% of the initiatives specifically collected data on
   IAS of Union Concern, citizen science in Europe is of policy relevance.
   Despite this, only half of the projects indicated sustainable funding.
   Nearly all projects had validation in place to verify species
   identifications. Strikingly, only about one third of the projects shared
   their data with open data repositories such as the Global Biodiversity
   Information Facility or the European Alien Species Information Network.
   Moreover, many did not adhere to the principles of FAIR data management.
   Finally, certain factors of engagement, feedback and support, had
   significant impacts on project performance, with the provision of a map
   with sightings being especially beneficial. Based on this dataset, we
   offer suggestions to strengthen the network of IAS citizen science
   projects and to foster knowledge exchange among citizens, scientists,
   managers, policy-makers, local authorities, and other stakeholders.},
Publisher = {PENSOFT PUBLISHERS},
Address = {12 PROF GEORGI ZLATARSKI ST, SOFIA, 1700, BULGARIA},
Type = {Article},
Language = {English},
Affiliation = {Marchante, E (Corresponding Author), Univ Coimbra, Ctr Funct Ecol, Dept Life Sci, Coimbra, Portugal.
   Price-Jones, Veronica; Brown, Peter M. J., Anglia Ruskin Univ, Sch Life Sci, Cambridge, England.
   Adriaens, Tim, Res Inst Nat \& Forest INBO, Brussels, Belgium.
   Tricarico, Elena, Univ Florence, Dept Biolog, Sesto Fiorentino, FI, Italy.
   Cardoso, Ana Cristina; Gervasini, Eugenio; Schade, Sven; Tsinaraki, Chrisa, European Alien Species Informat Network EASIN, European Commiss Joint Res Ctr, Ispra, Italy.
   Groom, Quentin, Meise Bot Garden, Meise, Belgium.
   Marchante, Elizabete, Univ Coimbra, Ctr Funct Ecol, Dept Life Sci, Coimbra, Portugal.},
DOI = {10.3897/neobiota.78.81476},
ISSN = {1619-0033},
EISSN = {1314-2488},
Keywords = {survey; public engagement; non-native species; crowdsourcing; community
   science; biological recording},
Research-Areas = {Biodiversity \& Conservation; Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Biodiversity Conservation; Ecology},
Author-Email = {emarchante@uc.pt},
Affiliations = {Anglia Ruskin University; Research Institute for Nature \& Forest;
   University of Florence; European Commission Joint Research Centre; EC
   JRC ISPRA Site; Universidade de Coimbra},
ResearcherID-Numbers = {Marchante, Elizabete/D-3858-2011
   Adriaens, Tim/F-6936-2010
   },
ORCID-Numbers = {Marchante, Elizabete/0000-0003-1303-7489
   Adriaens, Tim/0000-0001-7268-4200
   Reyserhove, Lien/0000-0001-7484-9267
   Cardoso, Ana Cristina/0000-0002-0350-0727},
Funding-Acknowledgement = {COST (European Cooperation in Science and Technology)
   {[}ECOST-STSM-CA17122-42402, CA17122]},
Funding-Text = {This work was supported by Action CA17122 Increasing understanding of
   alien species through citizen science (Alien-CSI), supported by COST
   (European Cooperation in Science and Technology www.cost.eu) through
   workshops and a short term scientific mission
   (ECOST-STSM-CA17122-42402). We thank Tim Woods (ECSA), and the Flemish
   Knowledge centre for Citizen Science (SCivil) for disseminating the
   survey through their networks. We are grateful to all the project
   coordinators for filling the survey on citizen science initiatives: Alex
   Richter-Boix, Andrew Salisbury, Anna Gazda, Anne Goggin, Antonina dos
   Santos, Antonios Geropoulos, Ariadna Just, Balazs Karolyi, Baudewijn
   Ode, Benoit Lagier, Bernardo Duarte, Christian Ries, Christophe Bornand,
   Colette O'Flynn, Conrad Altmann, Daniel Doerler, Dave Kilbey, Diemer
   Vercayie, Dinka Matosevic, Elsa Quillery, Esra Per, Esther Hughes,
   Ferenc Lakatos, Francesco Tiralongo, Fredrik Dahl, Gabor Pozsgai, Hanna
   Koivula, Helen Roy, Helene Hennig, Helia Marchante, Henk Groenewoud,
   Hugo Renato Marques Garcia Calado, Ines Correia Rosa, Ioannis Giovos,
   Jan Marcin Weslawski, Jean-Louis Chapuis, Jirislav Skuhrovec, Jitka
   Svobodova, Jo Clark, Joao Encarnacao, Joao Loureiro, John Wilkin-son,
   Jessica Thevenot, Julie Bailey, Jurga Motiejunaite, Karel Chobot, Karel
   Schoon-vaere, Karolina Bacela-Spychalska, Katharina Dehnen-Schmutz,
   Katharina Lapin, Katrin Schneider, Kelly Martinou, Ladislav Pekarik,
   Luciana Zedda, Luis Gonzalez Rodriguez, Luis Reino, Maarten de Groot,
   Malin Strand, Marija Smederevac-Lalic, Marina Golivets, Markus
   Seppaelae, Michael Pocock, Michelle Cleary, Milica Jacimovic, Milvana
   Arko-Pijevac, Mirela Uzelac, Monica Moura, Negin Ebrahimi, Nicole
   Noeske, Niki Chartosia, Nir Stern, Noe Ferreira Rodriguez, Ofer
   Steinitz, Ondrej Zicha, Paolo Balistreri, Pavel Pipek, Pedro Anastacio,
   Periklis Kleitou, Philippe Jourde, Quentin Rome, Rafal Maciaszek, Rigers
   Bakiu, Rory Putman, Rosa Olivo del Amo, Rui Bo-telho, Rumen Tomov,
   Sandor Nagy, Sandro Bertolino, Sofie De Smedt, Sonja Desnica, Tamas
   Komives, Tarso Costa, Tatsiana Lipinskaya, Tom Evans, Toril L. Moen,
   Valeria Lencioni, Victor Zamfir. We thank Craig Hilborn for advice on
   the statistical analysis.},
Number-of-Cited-References = {72},
Times-Cited = {7},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {15},
Journal-ISO = {NeoBiota},
Doc-Delivery-Number = {6I6JU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000886238300001},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000487958500031,
Author = {Schubert, Chris and Seyerl, Georg and Sack, Katharina},
Title = {Dynamic Data Citation Service-Subset Tool for Operational Data
   Management},
Journal = {DATA},
Year = {2019},
Volume = {4},
Number = {3},
Month = {SEP},
Abstract = {In earth observation and climatological sciences, data and their data
   services grow on a daily basis in a large spatial extent due to the high
   coverage rate of satellite sensors, model calculations, but also by
   continuous meteorological in situ observations. In order to reuse such
   data, especially data fragments as well as their data services in a
   collaborative and reproducible manner by citing the origin source, data
   analysts, e.g., researchers or impact modelers, need a possibility to
   identify the exact version, precise time information, parameter, and
   names of the dataset used. A manual process would make the citation of
   data fragments as a subset of an entire dataset rather complex and
   imprecise to obtain. Data in climate research are in most cases
   multidimensional, structured grid data that can change partially over
   time. The citation of such evolving content requires the approach of
   ``dynamic data citation{''}. The applied approach is based on
   associating queries with persistent identifiers. These queries contain
   the subsetting parameters, e.g., the spatial coordinates of the desired
   study area or the time frame with a start and end date, which are
   automatically included in the metadata of the newly generated subset and
   thus represent the information about the data history, the data
   provenance, which has to be established in data repository ecosystems.
   The Research Data Alliance Data Citation Working Group (RDA Data
   Citation WG) summarized the scientific status quo as well as the state
   of the art from existing citation and data management concepts and
   developed the scalable dynamic data citation methodology of evolving
   data. The Data Centre at the Climate Change Centre Austria (CCCA) has
   implemented the given recommendations and offers since 2017 an
   operational service on dynamic data citation on climate scenario data.
   With the consciousness that the objective of this topic brings a lot of
   dependencies on bibliographic citation research which is still under
   discussion, the CCCA service on Dynamic Data Citation focused on the
   climate domain specific issues, like characteristics of data, formats,
   software environment, and usage behavior. The current effort beyond
   spreading made experiences will be the scalability of the
   implementation, e.g., towards the potential of an Open Data Cube
   solution.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Schubert, C (Corresponding Author), Climate Change Ctr Austria, Data Ctr, A-1190 Vienna, Austria.
   Schubert, Chris; Seyerl, Georg, Climate Change Ctr Austria, Data Ctr, A-1190 Vienna, Austria.
   Sack, Katharina, WU Vienna Univ Econ \& Business, Inst Econ Policy \& Ind Econ, A-1020 Vienna, Austria.},
DOI = {10.3390/data4030115},
Article-Number = {115},
EISSN = {2306-5729},
Keywords = {dynamic data citation; subset; data curation; persistent identifier;
   data provenance; metadata; versioning; query store; data sharing; FAIR
   principles},
Research-Areas = {Computer Science; Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Computer Science, Information Systems; Multidisciplinary Sciences},
Author-Email = {chris.schubert@ccca.ac.at},
Affiliations = {Vienna University of Economics \& Business},
ResearcherID-Numbers = {Schubert, Chris/AAH-8588-2021
   },
ORCID-Numbers = {Schubert, Chris/0000-0002-4971-2493},
Funding-Acknowledgement = {Austrian Federal Ministry of Education, Science and Research (bmbwf)
   under the Research Investment Programme (HRSM) within the project CCCA;
   Austrian Federal Ministry of Education, Science and Research (bmbwf)
   under the Research Investment Programme (HRSM) within the project
   GEOCLIM; ``RDA Europe 4.0{''} Project},
Funding-Text = {This CCCA Data Centre Infrastructure has received funding from the
   Austrian Federal Ministry of Education, Science and Research (bmbwf)
   under the Research Investment Programme (HRSM) within the project CCCA
   and GEOCLIM as well as in-kind contribution by ZAMG. The planned
   activities for the Earth Observation Data extension as option of RDA
   outputs will be funded by the ``RDA Europe 4.0{''} Project. Contracts
   and agreements are under preparation at the time of publishing this
   article.},
Number-of-Cited-References = {15},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Data},
Doc-Delivery-Number = {JA6NG},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000487958500031},
OA = {gold, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000860008300001,
Author = {Yu, Kai and Wang, Ye and Zheng, Yongqiang and Liu, Zekun and Zhang,
   Qingfeng and Wang, Siyu and Zhao, Qi and Zhang, Xiaolong and Li,
   Xiaoxing and Xu, Rui-Hua and Liu, Ze-Xian},
Title = {qPTM: an updated database for PTM dynamics in human, mouse, rat and
   yeast},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2023},
Volume = {51},
Number = {D1},
Pages = {D479-D487},
Month = {JAN 6},
Abstract = {Post-translational modifications (PTMs) are critical molecular
   mechanisms that regulate protein functions temporally and spatially in
   various organisms. Since most PTMs are dynamically regulated,
   quantifying PTM events under different states is crucial for
   understanding biological processes and diseases. With the rapid
   development of high-throughput proteomics technologies, massive
   quantitative PTM proteome datasets have been generated. Thus, a
   comprehensive one-stop data resource for surfing big data will benefit
   the community. Here, we updated our previous phosphorylation dynamics
   database qPhos to the qPTM (http:// qptm.omicsbio.info). In qPTM, 11 482
   553 quantification events among six types of PTMs, including
   phosphorylation, acetylation, glycosylation, methylation, SUMOylation
   and ubiquitylation in four different organisms were collected and
   integrated, and the matched proteome datasets were included if
   available. The raw mass spectrometry based false discovery rate control
   and the recurrences of identifications among datasets were integrated
   into a scoring system to assess the reliability of the PTM sites. Browse
   and search functions were improved to facilitate users in swiftly and
   accurately acquiring specific information. The results page was revised
   with more abundant annotations, and time-course dynamics data were
   visualized in trend lines. We expected the qPTM database to be a much
   more powerful and comprehensive data repository for the PTM research
   community.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Xu, RH; Liu, ZX (Corresponding Author), Sun Yat Sen Univ, Canc Ctr, Collaborat Innovat Ctr Canc Med, State Key Lab Oncol South China, Guangzhou 510060, Peoples R China.
   Xu, RH (Corresponding Author), Chinese Acad Med Sci, Res Unit Precis Diag \& Treatment Gastrointestinal, Guangzhou 510060, Peoples R China.
   Yu, Kai; Wang, Ye; Zheng, Yongqiang; Liu, Zekun; Zhang, Qingfeng; Wang, Siyu; Zhao, Qi; Zhang, Xiaolong; Xu, Rui-Hua; Liu, Ze-Xian, Sun Yat Sen Univ, Canc Ctr, Collaborat Innovat Ctr Canc Med, State Key Lab Oncol South China, Guangzhou 510060, Peoples R China.
   Li, Xiaoxing, Sun Yat Sen Univ, Affiliated Hosp 1, Precis Med Inst, Guangzhou 510080, Peoples R China.
   Xu, Rui-Hua, Chinese Acad Med Sci, Res Unit Precis Diag \& Treatment Gastrointestinal, Guangzhou 510060, Peoples R China.},
DOI = {10.1093/nar/gkac820},
EarlyAccessDate = {SEP 2022},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PROTEIN POSTTRANSLATIONAL MODIFICATIONS; PROTEOGENOMIC CHARACTERIZATION;
   DATA-RESOURCE; IDENTIFICATION; METHYLATION; PHOSPHORYLATION; CROSSTALK;
   UBIQUITIN; NETWORKS; CANCER},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {xurh@sysucc.org.cn
   liuzx@sysucc.org.cn},
Affiliations = {State Key Lab Oncology South China; Sun Yat Sen University; Sun Yat Sen
   University; Chinese Academy of Medical Sciences - Peking Union Medical
   College},
ResearcherID-Numbers = {Li, Xiao-xing/B-9114-2008
   Zheng, Yongqiang/JGE-2907-2023
   Zhao, Qi/X-7899-2019
   Zhang, Xiaolong/AAS-4025-2020
   Liu, Zexian/D-1153-2011
   },
ORCID-Numbers = {Li, Xiao-xing/0000-0001-8791-7505
   Zheng, Yongqiang/0000-0003-3246-2800
   Zhao, Qi/0000-0002-8683-6145
   Liu, Zexian/0000-0001-9698-0610
   Yu, Kai/0000-0003-3343-2902},
Funding-Acknowledgement = {National Key R\&D Program of China {[}2021YFA1302100]; National Natural
   Science Foundation of China {[}81972239, 91953123, 81930065, 82173128];
   Science and Technology Program of Guangzhou {[}202206080011]; Program
   for Guangdong Introducing Innovative and Entrepreneurial Teams
   {[}2017ZT07S096]; Tip-Top Scientific and Technical Innovative Youth
   Talents of Guangdong Special Support Program {[}2019TQ05Y351]; Science
   and Technology Program of Guangdong {[}2019B020227002]; Natural Science
   Foundation of Guangdong Province {[}2019A1515010634]; CAMS Innovation
   Fund for Medical Sciences (CIFMS) {[}2019-I2M-5-036]},
Funding-Text = {National Key R\&D Program of China {[}2021YFA1302100]; National Natural
   Science Foundation of China {[}81972239,91953123, 81930065, 82173128];
   Science and Technology Program of Guangzhou {[}202206080011]; Program
   for Guangdong Introducing Innovative and Entrepreneurial Teams
   {[}2017ZT07S096]; Tip-Top Scientific and Technical Innovative Youth
   Talents of Guangdong Special Support Program {[}2019TQ05Y351]; Science
   and Technology Program of Guangdong {[}2019B020227002]; Natural Science
   Foundation of Guangdong Province {[}2019A1515010634]; CAMS Innovation
   Fund for Medical Sciences (CIFMS) {[}2019-I2M-5-036]. Funding for open
   access charge: National Key R\&D Program of China {[}2021YFA1302100].
   Conflict of interest statement. None declared.},
Number-of-Cited-References = {77},
Times-Cited = {8},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {Q5NY7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000860008300001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000600339800005,
Author = {Olakunde, Babayemi O. and Pharr, Jennifer R. and Chien, Lung-Chang and
   Benfield, Rebecca D. and Sy, Francisco S.},
Title = {Individual- and country-level correlates of female permanent
   contraception use in sub-Saharan Africa},
Journal = {PLOS ONE},
Year = {2020},
Volume = {15},
Number = {12},
Month = {DEC 15},
Abstract = {Background Female permanent contraception is a cost-effective
   contraceptive method that can help clients with the desire to limit
   childbearing achieve their reproductive intention. However, despite its
   benefits, the use of FPC remains low in sub-Saharan Africa (SSA), and
   limited studies have examined the correlates of its uptake. In this
   study, we assessed the individual- and country-level factors associated
   with the use of FPC among married or in-union women using modern
   contraceptive methods to limit childbearing in SSA.
   Methods This study was a secondary data analysis of individual- and
   country-level data obtained from the Demographic and Health Surveys
   (DHS) Program and three open data repositories. The study included
   29,777 married or in-union women aged 15-49 years using modern
   contraceptive methods to limit childbearing from DHS conducted in 33
   sub-Sahara African countries between 2010 and 2018. We performed
   descriptive statistics and fitted multilevel logistic regression models
   to determine the predisposing, enabling, and need factors associated
   with the use of FPC.
   Results Approximately 13\% of the women used FPC. About 20\% of the
   variance in the odds of using FPC was attributable to between-country
   differences. In the full model, the significant individual-level factors
   associated with the use of FPC compared with other modern contraceptive
   methods were: age (odds ratio {[}OR] = 1.10; 95\%CI = 1.08-1.12), living
   children (OR = 1.11, 95\%CI = 1.04-1.16), high household wealth (OR =
   1.39, 95\%CI = 1.18-1.64), rural residence (OR = 0.83, 95\% CI =
   0.71-0.97), joint contraceptive decision with partner (OR = 1.68, 95\% =
   1.43-1.99), contraceptive decision by partner and others (OR = 2.46,
   95\% = 1.97-3.07), and the number of living children less than the ideal
   number of children (OR = 1.40, 95\%CI = 1.21-1.62). The significantly
   associated country-level factors were births attended by skilled health
   providers (OR = 1.03, 95\%CI = 1.00-1.05) and density of medical doctors
   (OR = 1.37, 95\%CI = 1.01-1.85).
   Conclusions Our results suggest that both individual- and country-level
   factors affect uptake of FPC in SSA. Increasing geographic, economic,
   and psychosocial access to FPC may improve its uptake in SSA.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Olakunde, BO (Corresponding Author), Univ Nevada, Sch Publ Hlth, Dept Environm \& Occupat Hlth, Las Vegas, NV 89154 USA.
   Olakunde, BO (Corresponding Author), Natl Agcy Control AIDS, Dept Community Prevent \& Care Serv, Abuja, Nigeria.
   Olakunde, Babayemi O.; Pharr, Jennifer R.; Sy, Francisco S., Univ Nevada, Sch Publ Hlth, Dept Environm \& Occupat Hlth, Las Vegas, NV 89154 USA.
   Olakunde, Babayemi O., Natl Agcy Control AIDS, Dept Community Prevent \& Care Serv, Abuja, Nigeria.
   Chien, Lung-Chang, Univ Nevada, Sch Publ Hlth, Dept Epidemiol \& Biostat, Las Vegas, NV 89154 USA.
   Benfield, Rebecca D., Univ Nevada, Sch Nursing, Las Vegas, NV 89154 USA.},
DOI = {10.1371/journal.pone.0243316},
Article-Number = {e0243316},
ISSN = {1932-6203},
Keywords-Plus = {MULTILEVEL LOGISTIC-REGRESSION; BRIEF CONCEPTUAL TUTORIAL;
   TUBAL-LIGATION; SOCIAL EPIDEMIOLOGY; FERTILITY DESIRES;
   BEHAVIORAL-MODEL; STERILIZATION; WOMEN; ACCESS; HEALTH},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {olakunde@unlv.nevada.edu},
Affiliations = {Nevada System of Higher Education (NSHE); University of Nevada Las
   Vegas; Nevada System of Higher Education (NSHE); University of Nevada
   Las Vegas; Nevada System of Higher Education (NSHE); University of
   Nevada Las Vegas},
ORCID-Numbers = {Pharr, Jennifer/0000-0002-0383-2641},
Number-of-Cited-References = {71},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {PH3TP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000600339800005},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000433056900002,
Author = {Kim, Taemook and Seo, Hogyu David and Hennighausen, Lothar and Lee,
   Daeyoup and Kang, Keunsoo},
Title = {Octopus-toolkit: a workflow to automate mining of public epigenomic and
   transcriptomic next-generation sequencing data},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2018},
Volume = {46},
Number = {9},
Month = {MAY 18},
Abstract = {Octopus-toolkit is a stand-alone application for retrieving and
   processing large sets of next-generation sequencing (NGS) data with a
   single step. Octopus-toolkit is an automated set-up-and-analysis
   pipeline utilizing the Aspera, SRA Toolkit, FastQC, Trimmomatic, HISAT2,
   STAR, Samtools, and HOMER applications. All the applications are
   installed on the user's computer when the program starts. Upon the
   installation, it can automatically retrieve original files of various
   epigenomic and transcriptomic data sets, including ChIP-seq, ATAC-seq,
   DNase-seq, MeDIP-seq, MNase-seq and RNA-seq, from the gene expression
   omnibus data repository. The downloaded files can then be sequentially
   processed to generate BAM and BigWig files, which are used for advanced
   analyses and visualization. Currently, it can process NGS data from
   popular model genomes such as, human (Homo sapiens), mouse (Mus
   musculus), dog (Canis lupus familiaris), plant (Arabidopsis thaliana),
   zebrafish (Danio rerio), fruit fly (Drosophila melanogaster), worm
   (Caenorhabditis elegans), and budding yeast (Saccharomyces cerevisiae)
   genomes. With the processed files from Octopus-toolkit, the
   meta-analysis of various data sets, motif searches for DNA-binding
   proteins, and the identification of differentially expressed genes
   and/or protein-binding sites can be easily conducted with few commands
   by users. Overall, Octopus-toolkit facilitates the systematic and
   integrative analysis of available epigenomic and transcriptomic NGS big
   data.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Lee, D (Corresponding Author), Korea Adv Inst Sci \& Technol, Dept Biol Sci, Daejeon 34141, South Korea.
   Kang, K (Corresponding Author), Dankook Univ, Dept Microbiol, Cheonan 31116, South Korea.
   Kim, Taemook; Seo, Hogyu David; Lee, Daeyoup, Korea Adv Inst Sci \& Technol, Dept Biol Sci, Daejeon 34141, South Korea.
   Hennighausen, Lothar, NIDDK, Lab Genet \& Physiol, NIH, Bethesda, MD 20892 USA.
   Kang, Keunsoo, Dankook Univ, Dept Microbiol, Cheonan 31116, South Korea.},
DOI = {10.1093/nar/gky083},
Article-Number = {e53},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {SACCHAROMYCES-CEREVISIAE; HUMAN GENOME; RNA-SEQ; CHROMATIN; ALIGNER;
   GENES; STAT5},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {dylee@kaist.ac.kr
   kangk1204@gmail.com},
Affiliations = {Korea Advanced Institute of Science \& Technology (KAIST); National
   Institutes of Health (NIH) - USA; NIH National Institute of Diabetes \&
   Digestive \& Kidney Diseases (NIDDK); Dankook University},
ResearcherID-Numbers = {Seo, Hogyu David/AAC-7382-2021
   Lee, Daeyoup/C-1653-2011
   },
ORCID-Numbers = {Lee, Daeyoup/0000-0003-2006-1823
   Kang, Keunsoo/0000-0003-0611-9320},
Funding-Acknowledgement = {National R\&D Program for Cancer Control, Ministry of Health \& Welfare,
   Republic of Korea - Ministry of Science and ICT {[}1720100]; Mid-career
   Researcher Program through the National Research Foundation of Korea
   (NRF) - Ministry of Science and ICT {[}2016R1A2B2006354]},
Funding-Text = {National R\&D Program for Cancer Control, Ministry of Health \& Welfare,
   Republic of Korea {[}1720100]; Mid-career Researcher Program through the
   National Research Foundation of Korea (NRF) {[}2016R1A2B2006354] funded
   by the Ministry of Science and ICT. Funding for open access charge:
   National R\&D Program for Cancer Control, Ministry of Health \& Welfare,
   Republic of Korea {[}1720100]; Mid-career Researcher Program through the
   National Research Foundation of Korea (NRF) {[}2016R1A2B2006354] funded
   by the Ministry of Science and ICT.},
Number-of-Cited-References = {23},
Times-Cited = {41},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {44},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {GG9YK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000433056900002},
OA = {gold, Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000743496700094,
Author = {Dai, Die and Zhu, Jiaying and Sun, Chuqing and Li, Min and Liu, Jinxin
   and Wu, Sicheng and Ning, Kang and He, Li-Jie and Zhao, Xing-Ming and
   Chen, Wei-Hua},
Title = {GMrepo v2: a curated human gut microbiome database with special focus on
   disease markers and cross-dataset comparison},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2022},
Volume = {50},
Number = {D1},
Pages = {D777-D784},
Month = {JAN 7},
Abstract = {GMrepo (data repository for Gut Microbiota) is a database of curated and
   consistently annotated human gut metagenomes. Its main purposes are to
   increase the reusability and accessibility of human gut metagenomic
   data, and enable cross-project and phenotype comparisons. To achieve
   these goals, we performed manual curation on the meta-data and organized
   the datasets in a phenotype-centric manner. GMrepo v2 contains 353
   projects and 71,642 runs/samples, which are significantly increased from
   the previous version. Among these runs/samples, 45,111 and 26,531 were
   obtained by 16S rRNA amplicon and whole-genome metagenomics sequencing,
   respectively. We also increased the number of phenotypes from 92 to 133.
   In addition, we introduced disease-marker identification and
   cross-project/phenotype comparison. We first identified disease markers
   between two phenotypes (e.g. health versus diseases) on a per-project
   basis for selected projects. We then compared the identified markers for
   each phenotype pair across datasets to facilitate the identification of
   consistent microbial markers across datasets. Finally, we provided a
   marker-centric view to allow users to check if a marker has different
   trends in different diseases. So far, GMrepo includes 592 marker taxa
   (350 species and 242 genera) for 47 phenotype pairs, identified from 83
   selected projects. GMrepo v2 is freely available at:
   https://gmrepo.humangut.info.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Chen, WH (Corresponding Author), Huazhong Univ Sci \& Technol, Coll Life Sci \& Technol, Ctr Artificial Intelligence Biol,Minist Educ,Hube, Dept Bioinformat \& Syst Biol,Key Lab Mol Biophys, Wuhan, Peoples R China.
   Zhao, XM (Corresponding Author), Fudan Univ, Inst Sci \& Technol Brain Inspired Intelligence, Shanghai 200433, Peoples R China.
   He, LJ (Corresponding Author), China Med Univ, Peoples Hosp Liaoning Prov, Dept Oncol, Shenyang 110016, Peoples R China.
   Zhao, XM (Corresponding Author), Minist Educ, Key Lab Computat Neurosci \& Brain Inspired Intell, Shanghai, Peoples R China.
   Zhao, XM (Corresponding Author), Fudan Univ, Res Inst Intelligent Complex Syst, Shanghai 200433, Peoples R China.
   Chen, WH (Corresponding Author), Binzhou Med Univ, Inst Med Artificial Intelligence, Yantai 264003, Peoples R China.
   Dai, Die; Zhu, Jiaying; Sun, Chuqing; Li, Min; Wu, Sicheng; Ning, Kang; Chen, Wei-Hua, Huazhong Univ Sci \& Technol, Coll Life Sci \& Technol, Ctr Artificial Intelligence Biol,Minist Educ,Hube, Dept Bioinformat \& Syst Biol,Key Lab Mol Biophys, Wuhan, Peoples R China.
   Liu, Jinxin; Zhao, Xing-Ming, Fudan Univ, Inst Sci \& Technol Brain Inspired Intelligence, Shanghai 200433, Peoples R China.
   He, Li-Jie, China Med Univ, Peoples Hosp Liaoning Prov, Dept Oncol, Shenyang 110016, Peoples R China.
   Zhao, Xing-Ming, Minist Educ, Key Lab Computat Neurosci \& Brain Inspired Intell, Shanghai, Peoples R China.
   Zhao, Xing-Ming, Fudan Univ, Res Inst Intelligent Complex Syst, Shanghai 200433, Peoples R China.
   Chen, Wei-Hua, Binzhou Med Univ, Inst Med Artificial Intelligence, Yantai 264003, Peoples R China.},
DOI = {10.1093/nar/gkab1019},
EarlyAccessDate = {NOV 2021},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {LINKING},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {17702488896@163.com
   zmzhao@fudan.edu.cn
   weihuachen@hust.edu.cn},
Affiliations = {Huazhong University of Science \& Technology; Fudan University; China
   Medical University; Fudan University; Binzhou Medical University},
ResearcherID-Numbers = {Chen, Weihua/GRS-9256-2022
   Ning, Kang/ABD-3446-2020
   },
ORCID-Numbers = {Ning, Kang/0000-0003-3325-5387
   Chen, Wei-Hua/0000-0003-2168-6147
   Chen, Weihua/0000-0001-5160-4398
   , delicia/0000-0001-5309-8046
   Zhu, Jiaying/0000-0001-5247-7829},
Funding-Acknowledgement = {National Key Research and Development Program of China
   {[}2019YFA0905600]; National Natural Science Foundation of China
   {[}81803850, 61932008, 61772368]; National Key R\&D Program of China
   {[}2020YFA0712403]; Shanghai Science and Technology Innovation Fund
   {[}19511101404]; Shanghai Municipal Science and Technology Major Project
   {[}2018SHZDZX01]},
Funding-Text = {National Key Research and Development Program of China {[}2019YFA0905600
   toW.H.C.]; NationalNatural Science Foundation of China {[}81803850 to
   D.D., 61932008, 61772368 to X.M.Z.]; National Key R\&D Program of China
   {[}2020YFA0712403 to X.M.Z.]; Shanghai Science and Technology Innovation
   Fund {[}19511101404 to X.M.Z.]; ShanghaiMunicipal Science and Technology
   Major Project {[}2018SHZDZX01 to X.M.Z.]. Funding for open access
   charge: National Key Research and Development Program of China
   {[}2019YFA0905600 to W.H.C.].},
Number-of-Cited-References = {60},
Times-Cited = {32},
Usage-Count-Last-180-days = {9},
Usage-Count-Since-2013 = {38},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {YH9RO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000743496700094},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000634818900001,
Author = {Johansson Blixt, Patrik and Chew, Michelle S. and Ahman, Rasmus and de
   Geer, Lina and Blomqwist, Lill and Astrom Aneq, Meriam and Engvall, Jan
   and Andersson, Henrik},
Title = {Left ventricular longitudinal wall fractional shortening accurately
   predicts longitudinal strain in critically ill patients with septic
   shock},
Journal = {ANNALS OF INTENSIVE CARE},
Year = {2021},
Volume = {11},
Number = {1},
Month = {MAR 30},
Abstract = {Background Left ventricular longitudinal strain (LVLS) may be a
   sensitive indicator of left ventricular (LV) systolic function in
   patients with sepsis, but is dependent on high image quality and
   analysis software. Mitral annular plane systolic excursion (MAPSE) and
   the novel left ventricular longitudinal wall fractional shortening
   (LV-LWFS) are bedside echocardiographic indicators of LV systolic
   function that are less dependent on image quality. Both are sparsely
   investigated in the critically ill population, and may potentially be
   used as surrogates for LVLS. We assessed if LVLS may be predicted by
   LV-LWFS and MAPSE in patients with septic shock. We also assessed the
   repeatability and inter-rater agreement of LVLS, LV-LWFS and MAPSE
   measurements. Results 122 TTE studies from 3 echocardiographic data
   repositories of patients admitted to ICU with septic shock were
   retrospectively assessed, of which 73 were suitable for LVLS analysis
   using speckle tracking. The correlations between LVLS vs. LV-LWFS and
   LVLS vs. MAPSE were 0.89 (p < 0.001) and 0.81 (p < 0.001) with mean
   squared errors of 5.8\% and 9.1\%, respectively. Using the generated
   regression equation, LV-LWFS predicted LVLS with a high degree of
   accuracy and precision, with bias and limits of agreement of -0.044 +/-
   4.7\% and mean squared prediction error of 5.8\%. Interobserver
   repeatability was good, with high intraclass correlation coefficients
   (0.96-0.97), small bias and tight limits of agreement (<= 4.1\% for all
   analyses) between observers for all measurements. Conclusions LV-LWFS
   may be used to estimate LVLS in patients with septic shock. MAPSE also
   performed well, but was slightly inferior compared to LV-LWFS in
   estimating LVLS. Feasibility of MAPSE and LV-LWFS was excellent, as was
   interobserver repeatability.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Blixt, PJ (Corresponding Author), Linkoping Univ, Dept Anaesthesiol \& Intens Care, Biomed \& Clin Sci, S-58185 Linkoping, Sweden.
   Johansson Blixt, Patrik; Chew, Michelle S.; Ahman, Rasmus; de Geer, Lina; Andersson, Henrik, Linkoping Univ, Dept Anaesthesiol \& Intens Care, Biomed \& Clin Sci, S-58185 Linkoping, Sweden.
   Blomqwist, Lill, Skane Univ Hosp, Dept Anaesthesiol \& Intens Care, Malmo, Sweden.
   Astrom Aneq, Meriam; Engvall, Jan, Linkoping Univ, Dept Clin Physiol, Linkoping, Sweden.
   Astrom Aneq, Meriam; Engvall, Jan, Linkoping Univ, Dept Hlth Med \& Caring Sci, Linkoping, Sweden.
   Engvall, Jan, Linkoping Univ, Ctr Med Image Sci \& Visualizat, Linkoping, Sweden.},
DOI = {10.1186/s13613-021-00840-6},
Article-Number = {52},
ISSN = {2110-5820},
Keywords = {Strain; Fractional shortening; MAPSE; Left ventricle; Systolic function;
   Sepsis},
Keywords-Plus = {SPECKLE-TRACKING ECHOCARDIOGRAPHY; PLANE SYSTOLIC EXCURSION; INDUCED
   CARDIAC DYSFUNCTION; SEVERE SEPSIS; MORTALITY; MAPSE},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Critical Care Medicine},
Author-Email = {patbl790@student.liu.se},
Affiliations = {Linkoping University; Lund University; Skane University Hospital;
   Linkoping University; Linkoping University; Linkoping University},
ResearcherID-Numbers = {Engvall, Jan/I-5019-2019
   },
ORCID-Numbers = {Engvall, Jan/0000-0002-5716-5098
   Andersson, Henrik/0000-0002-6020-5177
   Johansson Blixt, Patrik/0000-0002-2870-6772},
Funding-Acknowledgement = {Linkoping University; Region Ostergotland ALF; Linkoping University
   {[}SC-2019-00155-12, LIO-935252, LIO-900161]},
Funding-Text = {Open access funding provided by Linkoping University. This study was
   partly funded by grants from the Region Ostergotland ALF grants and
   Linkoping University (SC-2019-00155-12, LIO-935252, and LIO-900161). The
   funding bodies had no role in the design of the study and collection,
   analysis, and interpretation of data and in writing the manuscript.},
Number-of-Cited-References = {28},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Ann. Intensive Care},
Doc-Delivery-Number = {RF4OF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000634818900001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000532084200037,
Author = {Malicki, Mario and Aalbersberg, IJsbrand Jan and Bouter, Lex and ter
   Riet, Gerben},
Title = {Journals' instructions to authors: A cross-sectional study across
   scientific disciplines},
Journal = {PLOS ONE},
Year = {2019},
Volume = {14},
Number = {9},
Month = {SEP 5},
Abstract = {In light of increasing calls for transparent reporting of research and
   prevention of detrimental research practices, we conducted a
   cross-sectional machine-assisted analysis of a representative sample of
   scientific journals' instructions to authors (ItAs) across all
   disciplines. We investigated addressing of 19 topics related to
   transparency in reporting and research integrity. Only three topics were
   addressed in more than one third of ItAs: conflicts of interest,
   plagiarism, and the type of peer review the journal employs. Health and
   Life Sciences journals, journals published by medium or large
   publishers, and journals registered in the Directory of Open Access
   Journals (DOAJ) were more likely to address many of the analysed topics,
   while Arts \& Humanities journals were least likely to do so. Despite
   the recent calls for transparency and integrity in research, our
   analysis shows that most scientific journals need to update their ItAs
   to align them with practices which prevent detrimental research
   practices and ensure transparent reporting of research.},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Malicki, M (Corresponding Author), Univ Amsterdam, Acad Med Ctr, Amsterdam UMC, Dept Cardiol, Amsterdam, Netherlands.
   Malicki, M (Corresponding Author), Amsterdam Univ Appl Sci, Fac Hlth, ACHIEVE Ctr Appl Res, Amsterdam, Netherlands.
   Malicki, Mario; ter Riet, Gerben, Univ Amsterdam, Acad Med Ctr, Amsterdam UMC, Dept Cardiol, Amsterdam, Netherlands.
   Malicki, Mario; ter Riet, Gerben, Amsterdam Univ Appl Sci, Fac Hlth, ACHIEVE Ctr Appl Res, Amsterdam, Netherlands.
   Aalbersberg, IJsbrand Jan, Elsevier, Amsterdam, Netherlands.
   Bouter, Lex, Vrije Univ Amsterdam, Dept Epidemiol \& Biostat, Amsterdam UMC, Med Ctr, Amsterdam, Netherlands.
   Bouter, Lex, Vrije Univ, Fac Humanities, Dept Philosophy, Amsterdam, Netherlands.},
DOI = {10.1371/journal.pone.0222157},
Article-Number = {e0222157},
ISSN = {1932-6203},
Keywords-Plus = {PUBLICATION},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {mario.malicki@mefst.hr},
Affiliations = {University of Amsterdam; Academic Medical Center Amsterdam; Vrije
   Universiteit Amsterdam; University of Amsterdam; Vrije Universiteit
   Amsterdam},
ResearcherID-Numbers = {Malički, Mario/E-8621-2016
   },
ORCID-Numbers = {Malički, Mario/0000-0003-0698-1930
   Bouter, Lex/0000-0002-2659-5482},
Funding-Acknowledgement = {Elsevier},
Funding-Text = {This study was a part of the Elsevierfunded project: Fostering
   Transparent and Responsible Conduct of Research: What can Journals do?.
   Details of the project are available at the project's data repository
   site: http://dx.doi.org/10.17632/53cskwwpdn.3.The Elsevier funding was
   awarded to GtR at Amsterdam University Medical Centers, location
   Meibergdreef, Amsterdam, The Netherlands, who in turn hired MM for a
   postdoc position and provided the salary for MM to work on the project.
   There was no additional external funding received for this study. The
   funders (other than the funder-affiliated author IJJA) had no role in
   study design, data collection and analysis, decision to publish, or
   preparation of the manuscript.},
Number-of-Cited-References = {51},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {PLoS One},
Doc-Delivery-Number = {LM2LR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000532084200037},
OA = {Green Published, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000714436200008,
Author = {Cheah, Yong Kang and Kee, Chee Cheong and Lim, Kuang Hock and Omar, Mohd
   Azahadi},
Title = {Mental health and risk behaviors among secondary school students: A
   study on ethnic minorities},
Journal = {PEDIATRICS AND NEONATOLOGY},
Year = {2021},
Volume = {62},
Number = {6},
Pages = {628-637},
Month = {NOV},
Abstract = {Background: Mental health disorders are highly correlated with risk
   behaviors. The objective of the present study is to examine the
   relationship between risk behaviors and mental health among school-going
   students with a focus on ethnic minorities. Methods: The National Health
   and Morbidity Survey (NHMS) 2017 (n Z 8230) was used for analyses. It
   was a nationwide survey conducted in Malaysia. The dependent variables
   were measured by three risk behaviors (cigarette smoking, alcohol
   drinking and use of illicit drugs). Probit regressions were utilized to
   examine the effect of mental health on the probability of smoking,
   drinking and using illicit drugs. Demographic and lifestyle factors were
   used as the control variables. Truancy was identified as a mediating
   variable. Results: Anxiety, depression and suicidal ideation affected
   cigarette smoking, alcohol drinking and use of illicit drugs through
   mediation of truancy. After controlling for demographic and lifestyle
   factors, students with anxiety, depression and suicidal ideation were
   more likely to smoke, drink and use illicit drugs compared with their
   peers without any mental health disorders. Furthermore, the likelihood
   of consuming cigarettes, alcohol and illicit drugs was found to be
   higher among students who played truant than those who did not.
   Conclusion: Mental health plays an important role in determining
   participation in risk behaviors among ethnic minority students in
   Malaysia. Public health administrators and schools have to be aware that
   students who suffer from mental health disorders are likely to indulge
   in risk behaviors. Copyright (c) 2021, Taiwan Pediatric Association.
   Published by Elsevier Taiwan LLC. This is an open access article under
   the CC BY-NC-ND license (http://creativecommons.org/licenses/
   by-nc-nd/4.0/).},
Publisher = {ELSEVIER TAIWAN},
Address = {RM N-412, 4F, CHIA HSIN BUILDING 11, NO 96, ZHONG SHAN N ROAD SEC 2,
   TAIPEI, 10449, TAIWAN},
Type = {Article},
Language = {English},
Affiliation = {Cheah, YK (Corresponding Author), Univ Utara Malaysia, Coll Business, Sch Econ Finance \& Banking, Sintok 06010, Kedah Darul Ama, Malaysia.
   Cheah, Yong Kang, Univ Utara Malaysia, Coll Business, Sch Econ Finance \& Banking, Sintok 06010, Kedah Darul Ama, Malaysia.
   Kee, Chee Cheong; Omar, Mohd Azahadi, Minist Hlth Malaysia, Sect Biostat \& Data Repository, Natl Inst Hlth, 1,Jln Setia Murni U13-52,Seksyen U13, Shah Alam 40170, Selangor, Malaysia.
   Lim, Kuang Hock, Minist Hlth Malaysia, Inst Med Res, Jalan Pahang, Kuala Lumpur 50588, Malaysia.},
DOI = {10.1016/j.pedneo.2021.05.025},
EarlyAccessDate = {OCT 2021},
ISSN = {1875-9572},
EISSN = {2212-1692},
Keywords = {adolescent; ethnicity; mental health; risk behavior; student},
Keywords-Plus = {ILLICIT DRUG-USE; ALCOHOL-USE; GOING ADOLESCENTS; POOR ATTENDANCE;
   SMOKING; DEPRESSION; ASSOCIATION; CONSUMPTION; PREVALENCE; PREDICTORS},
Research-Areas = {Pediatrics},
Web-of-Science-Categories  = {Pediatrics},
Author-Email = {yong@uum.edu.my},
Affiliations = {Universiti Utara Malaysia; Kementerian Kesihatan Malaysia; Kementerian
   Kesihatan Malaysia},
ResearcherID-Numbers = {Cheah, Yong Kang/M-2677-2014
   Chee Cheong, Kee/AAB-2971-2019},
ORCID-Numbers = {Cheah, Yong Kang/0000-0002-6793-7055
   Chee Cheong, Kee/0000-0003-1372-9549},
Number-of-Cited-References = {43},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Pediatr. Neonatol.},
Doc-Delivery-Number = {WR3XG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000714436200008},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000954807400001,
Author = {Miles, Victoria and Giani, Stefano and Vogt, Oliver},
Title = {Approaching STEP file analysis as a language processing task: A robust
   and scale-invariant solution for machining feature recognition},
Journal = {JOURNAL OF COMPUTATIONAL AND APPLIED MATHEMATICS},
Year = {2023},
Volume = {427},
Month = {AUG 1},
Abstract = {Machining feature recognition is a key task in the intelligent analysis
   of 3D CAD models as it represents a bridge between a part design and the
   manufacturing processes required for manufacture and can, therefore,
   increase automation in the manufacturing process. As 3D model files do
   not naturally conform to the fixed size necessary as the input to most
   varieties of neural network, most existing solutions for machining
   feature recognition rely on either transforming CAD models into a fixed
   shape representation, accepting some loss of information in the process,
   or employ rigid rules-based feature extraction techniques prior to
   applying any learning-based algorithm, resulting in solutions which may
   display high performance for specific applications but which lack in the
   flexibility provided by a purely learning-based approach. In this paper,
   we present a novel machining feature recognition model, which is capable
   of interpreting the data present in a STEP (standard for the exchange of
   product data) file using purely learning-based algorithms, with no need
   for human input. Our model builds on the basic framework for feature
   extraction from STEP file data proposed in Miles et al. (2022), with the
   design of a decoder network capable of using extracted features to
   perform the complex task of machining feature recognition. Model
   performance is evaluated based on accuracy at the task of identifying 24
   classes of machining feature in CAD models containing between two and
   ten intersecting features. Results demonstrate that our solution
   achieves comparable performance with existing solutions when given data
   similar to that used during training and significantly increased
   robustness when compared to existing solutions when presented with CAD
   models which vary from those seen during training and contain small
   features. (c) 2023 The Author(s). Published by Elsevier B.V. This is an
   open access article under the CC},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Miles, V (Corresponding Author), Univ Durham, Dept Engn, Stockton Rd, Durham DH1 3LE, England.
   Miles, Victoria; Giani, Stefano; Vogt, Oliver, Univ Durham, Dept Engn, Stockton Rd, Durham DH1 3LE, England.},
DOI = {10.1016/j.cam.2023.115166},
EarlyAccessDate = {MAR 2023},
Article-Number = {115166},
ISSN = {0377-0427},
EISSN = {1879-1778},
Keywords = {3D CAD; STEP files; Artificial intelligence; Recursive neural network;
   Recurrent neural network},
Keywords-Plus = {SYSTEM},
Research-Areas = {Mathematics},
Web-of-Science-Categories  = {Mathematics, Applied},
Author-Email = {victoria.s.miles@durham.ac.uk},
Affiliations = {Durham University},
ORCID-Numbers = {Miles, Victoria/0000-0002-2268-1471},
Funding-Acknowledgement = {Engineering and Physical Sciences Research Council (EPSRC) , United
   Kingdom {[}EP/T518001/1]},
Funding-Text = {Acknowledgements This work has used Durham University?s NCC cluster. NCC
   has been purchased through Durham University?s strategic investment
   funds, and is installed and maintained by the Department of Computer
   Science. This work was supported by the Engineering and Physical
   Sciences Research Council (EPSRC) , United Kingdom {[}grant number
   EP/T518001/1] . For the purpose of open access, the author has applied a
   Creative Commons Attribution (CC BY) licence to any Author Accepted
   Manuscript version arising. The dataset used in this paper can be
   accessed from the Durham Research Data Repository, at
   http://dx.doi.org/10.15128/r26q182k16s. The authors have no competing
   interests to declare.},
Number-of-Cited-References = {34},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Comput. Appl. Math.},
Doc-Delivery-Number = {A4JN3},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000954807400001},
OA = {Green Published, Green Accepted, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000483586700012,
Author = {Nair, Malavika and Calahorra, Yonatan and Kar-Narayan, Sohini and Best,
   Serena M. and Cameron, Ruth E.},
Title = {Self-assembly of collagen bundles and enhanced piezoelectricity induced
   by chemical crosslinking},
Journal = {NANOSCALE},
Year = {2019},
Volume = {11},
Number = {32},
Pages = {15120-15130},
Month = {AUG 28},
Abstract = {The piezoelectricity of collagen is purported to be linked to many
   biological processes including bone formation and wound healing.
   Although the piezoelectricity of tissue-derived collagen has been
   documented across the length scales, little work has been undertaken to
   characterise the local electromechanical properties of processed
   collagen, which is used as a base for tissue-engineering implants. In
   this work, three chemically distinct treatments used to form
   structurally and mechanically stable scaffolds-EDC-NHS, genipin and
   tissue transglutaminase-are investigated for their effect on collagen
   piezolectricity. Crosslinking with EDC-NHS is noted to produce a
   distinct self-assembly of the fibres into bundles roughly 300 nm in
   width regardless of the collagen origin. These fibre bundles also show a
   localised piezoelectric response, with enhanced vertical
   piezoelectricity of collagen. Such topographical features are not
   observed with the other two chemical treatments, although the shear
   piezoelectric response is significantly enhanced upon crosslinking.
   These observations are reconciled by a proposed effect of the
   crosslinking mechanisms on the molecular and nanostructure of collagen.
   These results highlight the ability to modify the electromechanical
   properties of collagen using chemical crosslinking methods.},
Publisher = {ROYAL SOC CHEMISTRY},
Address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS,
   ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Cameron, RE (Corresponding Author), Univ Cambridge, Dept Mat Sci \& Met, 27 Charles Babbage Rd, Cambridge CB3 0DS, England.
   Nair, Malavika; Calahorra, Yonatan; Kar-Narayan, Sohini; Best, Serena M.; Cameron, Ruth E., Univ Cambridge, Dept Mat Sci \& Met, 27 Charles Babbage Rd, Cambridge CB3 0DS, England.},
DOI = {10.1039/c9nr04750f},
ISSN = {2040-3364},
EISSN = {2040-3372},
Keywords-Plus = {IN-VITRO; MECHANICAL-PROPERTIES; GENIPIN},
Research-Areas = {Chemistry; Science \& Technology - Other Topics; Materials Science;
   Physics},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary; Nanoscience \& Nanotechnology; Materials
   Science, Multidisciplinary; Physics, Applied},
Author-Email = {smb51@cam.ac.uk
   rec11@cam.ac.uk},
Affiliations = {University of Cambridge},
ResearcherID-Numbers = {Kar-Narayan, Sohini/N-4103-2016
   Calahorra, Yonatan/H-9503-2019
   },
ORCID-Numbers = {Kar-Narayan, Sohini/0000-0002-8151-1616
   Calahorra, Yonatan/0000-0001-9530-1006
   Cameron, Ruth/0000-0003-1573-4923
   Best, Serena/0000-0001-7866-8607
   Nair, Malavika/0000-0002-5229-8991},
Funding-Acknowledgement = {ERC {[}639526]; EPSRC Established Career Fellowship {[}EP/N019938/1];
   Bill and Melinda Gates Foundation {[}OPP1144]; Gates Cambridge Trust;
   Geistlich Pharma AG; European Research Council (ERC) {[}639526] Funding
   Source: European Research Council (ERC); EPSRC {[}EP/N019938/1] Funding
   Source: UKRI},
Funding-Text = {SKN and YC acknowledge financial support from the ERC Starting Grant
   639526, NANOGEN. REC and SMB acknowledge the supported by the EPSRC
   Established Career Fellowship Grant No. EP/N019938/1. Open Access is
   funded by the Bill and Melinda Gates Foundation OPP1144. MN acknowledges
   the financial support provided by the Gates Cambridge Trust and
   Geistlich Pharma AG to undertake this research. Data is available on the
   University of Cambridge Apollo Open Data Repository at
   http://dx.doi.org/10.17863/CAM.40297.},
Number-of-Cited-References = {45},
Times-Cited = {23},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {45},
Journal-ISO = {Nanoscale},
Doc-Delivery-Number = {IU4WD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000483586700012},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000607612300011,
Author = {Kaur, Shraddha and Norris, Dennis G. and Gathercole, Susan E.},
Title = {The Time Course of Updating in Running Span},
Journal = {JOURNAL OF EXPERIMENTAL PSYCHOLOGY-LEARNING MEMORY AND COGNITION},
Year = {2020},
Volume = {46},
Number = {12},
Pages = {2397-2409},
Month = {DEC},
Abstract = {Running span can be performed by either passively listening to memory
   items or actively updating the target set. Previous research suggests
   that the active updating process is demanding and time consuming and is
   favored at slow rates of presentation while the passive strategy is
   employed at fast rates. Two experiments examined the time course of
   recruitment of resources during task performance and its sensitivity to
   presentation rate. In Experiment 1, participants performed 1 of 3 serial
   recall tasks: running span, simple span, and modified span. The tasks
   were completed at the same time as a choice reaction time (RT; CRT) task
   and the RTs were used to index the resource demands of the memory task.
   Running span generated higher RT costs than simple span. The costs were
   present only for positions at and beyond the point in the sequence when
   the target memory set was changed, indicating a shift to a more
   cognitively demanding mode of updating. At these positions there was a
   generalized increase in RT costs that peaked 1,000 ms following item
   presentation. In Experiment 2 the resource demands of running span
   varied with presentation rate and a peak demand at 1,000 ms was again
   evident, but only with a slow presentation rate. In conjunction with
   strategy reports, these data establish that the process of active
   updating in running span is slow and cognitively demanding, making it
   difficult to use when presentation rates are fast.},
Publisher = {AMER PSYCHOLOGICAL ASSOC},
Address = {750 FIRST ST NE, WASHINGTON, DC 20002-4242 USA},
Type = {Article},
Language = {English},
Affiliation = {Kaur, S (Corresponding Author), Alzheimers Soc, 43-44 Crutched Friars, London EC3N 2AE, England.
   Kaur, Shraddha; Norris, Dennis G.; Gathercole, Susan E., Univ Cambridge, Cognit \& Brain Sci Unit, MRC, Cambridge, England.
   Gathercole, Susan E., Univ Cambridge, Dept Psychiat, Cambridge, England.},
DOI = {10.1037/xlm0000800},
ISSN = {0278-7393},
EISSN = {1939-1285},
Keywords = {running span; working memory updating; cognitive demand; working memory},
Keywords-Plus = {WORKING-MEMORY CAPACITY; NETWORK MODEL; ATTENTION},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology; Psychology, Experimental},
Author-Email = {Shraddha.Kaur@alzheimers.org.uk},
Affiliations = {University of Cambridge; University of Cambridge},
Funding-Acknowledgement = {Medical Research Council of Great Britain; University of Cambridge;
   Gates-Cambridge Trust {[}BMGF OPP1144]; MRC {[}MC\_UU\_00005/11] Funding
   Source: UKRI},
Funding-Text = {This work was supported by the Medical Research Council of Great
   Britain, the University of Cambridge and the Gates-Cambridge Trust (BMGF
   OPP1144). The data reported in this article will be made available in
   the CBU Open Data Repository
   (http://www.mrc-cbu.cam.ac.uk/publications/opendata).},
Number-of-Cited-References = {50},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {J. Exp. Psychol.-Learn. Mem. Cogn.},
Doc-Delivery-Number = {PS0IM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000607612300011},
OA = {Green Submitted, hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000462587400064,
Author = {Perez-Riverol, Yasset and Csordas, Attila and Bai, Jingwen and
   Bernal-Llinares, Manuel and Hewapathirana, Suresh and Kundu, Deepti J.
   and Inuganti, Avinash and Griss, Johannes and Mayer, Gerhard and
   Eisenacher, Martin and Perez, Enrique and Uszkoreit, Julian and
   Pfeuffer, Julianus and Sachsenberg, Timo and Yilmaz, Sule and Tiwary,
   Shivani and Cox, Juergen and Audain, Enrique and Walzer, Mathias and
   Jarnuczak, Andrew F. and Ternent, Tobias and Brazma, Alvis and Vizcaino,
   Juan Antonio},
Title = {The PRIDE database and related tools and resources in 2019: improving
   support for quantification data},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2019},
Volume = {47},
Number = {D1},
Pages = {D442-D450},
Month = {JAN 8},
Abstract = {The PRoteomics IDEntifications (PRIDE) database
   (https://www.ebi.ac.uk/pride/) is the world's largest data repository of
   mass spectrometry-based proteomics data, and is one of the founding
   members of the global ProteomeXchange (PX) consortium. In this
   manuscript, we summarize the developments in PRIDE resources and related
   tools since the previous update manuscript was published in Nucleic
   Acids Research in 2016. In the last 3years, public data sharing through
   PRIDE (as part of PX) has definitely become the norm in the field. In
   parallel, data re-use of public proteomics data has increased
   enormously, with multiple applications. We first describe the new
   architecture of PRIDE Archive, the archival component of PRIDE. PRIDE
   Archive and the related data submission framework have been further
   developed to support the increase in submitted data volumes and
   additional data types. A new scalable and fault tolerant storage
   backend, Application Programming Interface and web interface have been
   implemented, as a part of an ongoing process. Additionally, we emphasize
   the improved support for quantitative proteomics data through the mzTab
   format. At last, we outline key statistics on the current data contents
   and volume of downloads, and how PRIDE data are starting to be
   disseminated to added-value resources including Ensembl, UniProt and
   Expression Atlas.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Perez-Riverol, Y; Vizcaíno, JA (Corresponding Author), EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Perez-Riverol, Yasset; Csordas, Attila; Bai, Jingwen; Bernal-Llinares, Manuel; Hewapathirana, Suresh; Kundu, Deepti J.; Inuganti, Avinash; Griss, Johannes; Perez, Enrique; Walzer, Mathias; Jarnuczak, Andrew F.; Ternent, Tobias; Brazma, Alvis; Vizcaino, Juan Antonio, EBI, EMBL, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Griss, Johannes, Med Univ Vienna, Div Immunol Allergy \& Infect Dis, Dept Dermatol, A-1090 Vienna, Austria.
   Mayer, Gerhard; Eisenacher, Martin; Uszkoreit, Julian, Ruhr Univ Bochum, Med Fac, Med Proteom Ctr, D-44801 Bochum, Germany.
   Pfeuffer, Julianus; Sachsenberg, Timo, Univ Tubingen, Appl Bioinformat, Dept Comp Sci, Sand 14, D-72076 Tubingen, Germany.
   Yilmaz, Sule; Tiwary, Shivani; Cox, Juergen, Max Planck Inst Biochem, Computat Syst Biochem, D-82152 Martinsried, Germany.
   Audain, Enrique, Univ Klinikum Schleswig Holstein Kiel, Dept Congenital Heart Dis \& Pediat Cardiol, D-24105 Kiel, Germany.},
DOI = {10.1093/nar/gky1106},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {PROTEIN IDENTIFICATION; PROTEOMICS DATA; PROTEOMEXCHANGE; PLATFORM;
   VISUALIZATION; PEPTIDEATLAS; MULTIPLE; UPDATE},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {yperez@ebi.ac.uk
   juan@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL); Wellcome Trust Sanger
   Institute; Medical University of Vienna; Ruhr University Bochum;
   Eberhard Karls University of Tubingen; Max Planck Society; University of
   Kiel; Schleswig Holstein University Hospital},
ResearcherID-Numbers = {Perez-Riverol, Yasset/H-2873-2019
   Eisenacher, Martin/J-8044-2014
   Vizcaino, Juan Antonio/C-3691-2009
   Pérez Navarro, Enrique/E-5858-2019
   Uszkoreit, Julian/GQA-8317-2022
   Uszkoreit, Julian/AAD-1957-2021
   Perez, Enrique/R-6584-2019
   Cox, Jurgen/B-9481-2008
   Sachsenberg, Timo/AAN-9201-2020
   },
ORCID-Numbers = {Perez-Riverol, Yasset/0000-0001-6579-6941
   Eisenacher, Martin/0000-0003-2687-7444
   Vizcaino, Juan Antonio/0000-0002-3905-4335
   Pérez Navarro, Enrique/0000-0003-1091-8926
   Uszkoreit, Julian/0000-0001-7522-4007
   Uszkoreit, Julian/0000-0001-7522-4007
   Perez, Enrique/0000-0003-1091-8926
   Cox, Jurgen/0000-0001-8597-205X
   Sachsenberg, Timo/0000-0002-2833-6070
   Mayer, Gerhard/0000-0002-1767-2343
   Jarnuczak, Andrew/0000-0001-6368-3951
   Brazma, Alvis/0000-0001-5988-7409
   Walzer, Mathias/0000-0003-4538-2754
   Audain, Enrique/0000-0002-9201-7840
   Kundu, Deepti Jaiswal/0000-0003-2989-5971
   Griss, Johannes/0000-0003-2206-9511
   Bernal Llinares, Manuel/0000-0002-7368-180X
   Yilmaz-Rumpf, Sule/0000-0002-5329-3324
   Hewapathirana, Suresh/0000-0002-7862-5022},
Funding-Acknowledgement = {Wellcome Trust {[}WT101477MA, 208391/Z/17/Z]; BBSRC {[}BB/K01997X/1,
   BB/L024225/1, BB/P024599/1]; UK-Japan Partnership Award
   {[}BB/N022440/1]; NIH `Proteomics Standards' Grant {[}R24 GM127667-01];
   EU H2020 Project THOR {[}654039]; Three ELIXIR Implementation Studies;
   EMBL Core Funding; de.NBI Project of the German Federal Ministry of
   Education and Research (BMBF) {[}FKZ 031 A 534A, 031 A 535A]; Vienna
   Science and Technology Fund (WWTF) {[}LS11-045]; PURE (Protein research
   Unit Ruhr within Europe), a project of North Rhine-Westphalia, a federal
   state of Germany; European Union {[}686547]; FP7 {[}GA
   ERC2012-SyG318987-ToPAG]; BBSRC {[}BB/K01997X/1, BB/L024225/1,
   BB/N022440/1, BB/P024599/1] Funding Source: UKRI},
Funding-Text = {Wellcome Trust {[}WT101477MA, 208391/Z/17/Z]; BBSRC Grants `PROCESS'
   {[}BB/K01997X/1]; `ProteoGenomics' {[}BB/L024225/1]; `Proteomics DIA'
   {[}BB/P024599/1]; UK-Japan Partnership Award {[}BB/N022440/1]; NIH
   `Proteomics Standards' Grant {[}R24 GM127667-01]; EU H2020 Project THOR
   {[}654039]; Three ELIXIR Implementation Studies; EMBL Core Funding;
   de.NBI Project of the German Federal Ministry of Education and Research
   (BMBF) {[}FKZ 031 A 534A to G.M., 031 A 535A to J.P., T.S.]; Vienna
   Science and Technology Fund (WWTF) {[}LS11-045 to J.G.]; PURE (Protein
   research Unit Ruhr within Europe), a project of North Rhine-Westphalia,
   a federal state of Germany (to M.E.); European Union's Horizon 2020
   Research and Innovation Program {[}686547 to J.C.]; FP7 {[}GA
   ERC2012-SyG318987-ToPAGtoS.T.]. Funding for open access charge: Wellcome
   Trust.},
Number-of-Cited-References = {40},
Times-Cited = {4761},
Usage-Count-Last-180-days = {12},
Usage-Count-Since-2013 = {128},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {HQ7GH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000462587400064},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000371261700064,
Author = {Sud, Manish and Fahy, Eoin and Cotter, Dawn and Azam, Kenan and
   Vadivelu, Ilango and Burant, Charles and Edison, Arthur and Fiehn,
   Oliver and Higashi, Richard and Nair, K. Sreekumaran and Sumner, Susan
   and Subramaniam, Shankar},
Title = {Metabolomics Workbench: An international repository for metabolomics
   data and metadata, metabolite standards, protocols, tutorials and
   training, and analysis tools},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2016},
Volume = {44},
Number = {D1},
Pages = {D463-D470},
Month = {JAN 4},
Abstract = {The Metabolomics Workbench, available at www.metabolomicsworkbench.org,
   is a public repository for metabolomics metadata and experimental data
   spanning various species and experimental platforms, metabolite
   standards, metabolite structures, protocols, tutorials, and training
   material and other educational resources. It provides a computational
   platform to integrate, analyze, track, deposit and disseminate large
   volumes of heterogeneous data from a wide variety of metabolomics
   studies including mass spectrometry (MS) and nuclear magnetic resonance
   spectrometry (NMR) data spanning over 20 different species covering all
   the major taxonomic categories including humans and other mammals,
   plants, insects, invertebrates and microorganisms. Additionally, a
   number of protocols are provided for a range of metabolite classes,
   sample types, and both MS and NMR-based studies, along with a metabolite
   structure database. The metabolites characterized in the studies
   available on the Metabolomics Workbench are linked to chemical
   structures in the metabolite structure database to facilitate
   comparative analysis across studies. The Metabolomics Workbench, part of
   the data coordinating effort of the National Institute of Health (NIH)
   Common Fund's Metabolomics Program, provides data from the Common Fund's
   Metabolomics Resource Cores, metabolite standards, and analysis tools to
   the wider metabolomics community and seeks data depositions from
   metabolomics researchers across the world.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Subramaniam, S (Corresponding Author), Univ Calif San Diego, San Diego Supercomp Ctr, 9500 Gilman Dr, La Jolla, CA 92037 USA.
   Subramaniam, S (Corresponding Author), Univ Calif San Diego, Dept Bioengn Comp Sci \& Engn, La Jolla, CA 92093 USA.
   Subramaniam, S (Corresponding Author), Univ Calif San Diego, Dept Cellular \& Mol Med, La Jolla, CA 92093 USA.
   Subramaniam, S (Corresponding Author), Univ Calif San Diego, Dept Chem \& Biochem, La Jolla, CA 92093 USA.
   Sud, Manish; Fahy, Eoin; Cotter, Dawn; Azam, Kenan; Vadivelu, Ilango; Subramaniam, Shankar, Univ Calif San Diego, San Diego Supercomp Ctr, 9500 Gilman Dr, La Jolla, CA 92037 USA.
   Burant, Charles, Univ Michigan, 6300 Brehm Tower,1000 Wall St, Ann Arbor, MI 48105 USA.
   Edison, Arthur, Univ Florida, 2250 Shealy Dr, Gainesville, FL 32608 USA.
   Fiehn, Oliver, Univ Calif Davis, 451 Hlth Sci Dr, Davis, CA 95616 USA.
   Higashi, Richard, Univ Kentucky, 789 S Limestone,521 Biopharm Bldg, Lexington, KY 40536 USA.
   Nair, K. Sreekumaran, Mayo Clin, 200 First St SW, Rochester, MN 55902 USA.
   Sumner, Susan, RTI Int, 3040 Cornwallis Rd, Res Triangle Pk, NC 27709 USA.
   Subramaniam, Shankar, Univ Calif San Diego, Dept Bioengn Comp Sci \& Engn, La Jolla, CA 92093 USA.
   Subramaniam, Shankar, Univ Calif San Diego, Dept Cellular \& Mol Med, La Jolla, CA 92093 USA.
   Subramaniam, Shankar, Univ Calif San Diego, Dept Chem \& Biochem, La Jolla, CA 92093 USA.},
DOI = {10.1093/nar/gkv1042},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MINIMUM REPORTING STANDARDS; BIOLOGICAL SAMPLES; SYSTEMS BIOLOGY;
   REQUIREMENTS; INFORMATION; CHEMISTRY; PATHWAYS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {shankar@ucsd.edu},
Affiliations = {University of California System; University of California San Diego;
   University of Michigan System; University of Michigan; State University
   System of Florida; University of Florida; University of California
   System; University of California Davis; University of Kentucky; Mayo
   Clinic; Research Triangle Institute; University of California System;
   University of California San Diego; University of California System;
   University of California San Diego; University of California System;
   University of California San Diego},
ResearcherID-Numbers = {Burant, Charles/GPC-5690-2022
   },
ORCID-Numbers = {Burant, Charles/0000-0001-9189-5003
   Edison, Arthur/0000-0002-5686-2350
   Sumner, Susan/0000-0003-3381-6084},
Funding-Acknowledgement = {National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
   of the National Institutes of Health (NIH) {[}U01 DK097430-01]; NIH
   Common Fund's Metabolomics ProgramMetabolomics Data Repository and
   Coordinating Center {[}1U01DK097430]},
Funding-Text = {National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK)
   of the National Institutes of Health (NIH) under award number U01
   DK097430-01. Funding to pay the Open Access publication charge was also
   provided by award number U01 DK097430-01. Funding for open access
   charge: NIH Common Fund's Metabolomics ProgramMetabolomics Data
   Repository and Coordinating Center {[}1U01DK097430].},
Number-of-Cited-References = {27},
Times-Cited = {418},
Usage-Count-Last-180-days = {10},
Usage-Count-Since-2013 = {150},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {DF3QY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000371261700064},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000871508100001,
Author = {Berlanga, Genesis and Williams, Quentin and Temiquel, Nathan},
Title = {Convolutional Neural Networks as a Tool for Roman Spectral Mineral
   Classification Under Low Signal, Dusty Mars Conditions},
Journal = {EARTH AND SPACE SCIENCE},
Year = {2022},
Volume = {9},
Number = {10},
Month = {OCT},
Abstract = {NASA's Mars 2020 and ESA's ExoMars will collect Raman measurements in
   dusty field conditions obscuring underlying rocks. This presents a
   challenge for remote Raman measurements at distances where mechanical or
   ablative sample cleaning is not straightforward. Historically, probing
   broad lithostratigraphic suites has been thwarted by the need for
   pristine targets and high-quality spectra. We provide a means of
   identifying Raman spectra of common rock-forming silicate, carbonate,
   and sulfate minerals under low signal-to-noise-ratios, Mars-like
   conditions using a convolutional neural network (CNN). The CNN was
   trained on the Machine Learning Raman Open Data set data set with
   500,000+ Raman spectra of hand samples/powder mixtures (5,000+
   spectra/mineral class). Diversity in sample microtopography,
   orientation, and crystallinity simulated varying laser focuses and
   spectral quality, and no traditional spectral preprocessing such as
   cosmic ray or baseline removal was employed. The CNN identified
   low-intensity Raman scatterers (micas and amphiboles), mixed minerals,
   and distinguished between mineral endmembers with +99\% success. We
   present among the first known implementations of ``big data{''} machine
   learning using varied, high-volume Raman spectral datasets. The pattern
   recognition abilities of CNNs can facilitate scientist Raman spectral
   interpretation on Earth and autonomous rover decision-making on planets
   like Mars; increasing scientific yield, correcting human classification
   errors, reducing the need for thorough target dust removal during
   evaluative measurements, and streamlining the data communications
   pipeline-saving time and resources. This study examines an end-to-end
   development process for creating a deep learning algorithm sensitive to
   varieties of Raman spectra and provides guidelines for CNN model
   development at the interface of Raman spectroscopy, deep learning, and
   planetary science.
   Plain Language Summary We collected thousands of spectra from rocks and
   minerals that are found on Earth and Mars and trained a computer to
   automatically identify them using an algorithm called a convolutional
   neural network or CNN. This is an effective but difficult algorithm to
   fine tune for Raman spectra as it requires a lot of training. A CNN
   works like an artificial brain with firing neurons. This brain can be
   uploaded onto Mars rovers such as NASA's Curiosity and Perseverance so
   that they can automatically identify rocks and minerals on Mars without
   human guidance. Doing this will accelerate scientific discovery while
   saving crucial mission time and energy. We essentially programmed the
   ``brains{''} of a rock and mineral identification ``tricorder{''}.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Berlanga, G (Corresponding Author), Univ Calif Santa Cruz, Dept Earth \& Planetary Sci, Santa Cruz, CA 95064 USA.
   Berlanga, G (Corresponding Author), NASA, BMSIS, Ames Res Ctr, Mountain View, CA 94043 USA.
   Berlanga, Genesis; Williams, Quentin, Univ Calif Santa Cruz, Dept Earth \& Planetary Sci, Santa Cruz, CA 95064 USA.
   Berlanga, Genesis, NASA, BMSIS, Ames Res Ctr, Mountain View, CA 94043 USA.
   Temiquel, Nathan, Coursera, Mountain View, CA USA.},
DOI = {10.1029/2021EA002125},
Article-Number = {e2021EA002125},
EISSN = {2333-5084},
Keywords-Plus = {LASER RAMAN-SPECTROSCOPY; MACHINE LEARNING TOOLS; INSTRUMENT SUITE;
   IDENTIFICATION; ROVER; SPECTROMETER; SUBTRACTION; RECOGNITION; FEATURES;
   SYSTEM},
Research-Areas = {Astronomy \& Astrophysics; Geology},
Web-of-Science-Categories  = {Astronomy \& Astrophysics; Geosciences, Multidisciplinary},
Author-Email = {genesis.berlanga@gmail.com},
Affiliations = {University of California System; University of California Santa Cruz;
   National Aeronautics \& Space Administration (NASA); NASA Ames Research
   Center},
ResearcherID-Numbers = {Williams, Quentin/HKF-3599-2023
   },
ORCID-Numbers = {Williams, Quentin/0000-0002-4798-5578
   Berlanga, Genesis/0000-0001-7666-6966
   Temiquel, Nathan/0000-0001-7734-0044},
Funding-Acknowledgement = {University of California Santa Cruz Department of Earth and Planetary
   Sciences; National Science Foundation {[}NSF-EAR2017294]},
Funding-Text = {The authors thank the University of California Santa Cruz Department of
   Earth and Planetary Sciences for internal support that made this work
   possible. Dr. Quentin Williams and the University of California Santa
   Cruz Raman Spectroscopy Laboratory are supported by the National Science
   Foundation grant NSF-EAR2017294. Special thanks to Dr. Patrick Gasda and
   Dr. Suniti Karunatillake for their careful manuscript reviews and
   suggestions, to the Editors of Earth and Space Science, and to Dr. Darby
   Dyar for insightful early manuscript feedback. The authors would also
   like to thank Dr. David Blake and Dr. Thomas Bristow for support with
   XRD analyses, Dr. Barbara LaFuente for support with code and data upload
   to the Open Data Repository, and Jamie Keith for project management
   support.},
Number-of-Cited-References = {96},
Times-Cited = {1},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Earth Space Sci.},
Doc-Delivery-Number = {5N0VE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000871508100001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000989437200001,
Author = {Chakrabarti, Anob M. M. and Capitanchik, Charlotte and Ule, Jernej and
   Luscombe, Nicholas M. M.},
Title = {<i>clipplotr</i>-a comparative visualization and analysis tool for CLIP
   data},
Journal = {RNA},
Year = {2023},
Volume = {29},
Number = {6},
Pages = {715-723},
Month = {JUN},
Abstract = {CLIP technologies are now widely used to study RNA-protein interactions
   and many data sets are now publicly available. An important first step
   in CLIP data exploration is the visual inspection and assessment of
   processed genomic data on selected genes or regions and performing
   comparisons: either across conditions within a particular project, or
   incorporating publicly available data. However, the output files
   produced by data processing pipelines or preprocessed files available to
   download from data repositories are often not suitable for direct
   comparison and usually need further processing. Furthermore, to derive
   biological insight it is usually necessary to visualize a CLIP signal
   alongside other data such as annotations, or orthogonal functional
   genomic data (e.g., RNA-seq). We have developed a simple, but powerful,
   command-line tool: clipplotr, which facilitates these visual comparative
   and integrative analyses with normalization and smoothing options for
   CLIP data and the ability to show these alongside reference annotation
   tracks and functional genomic data. These data can be supplied as input
   to clipplotr in a range of file formats, which will output a publication
   quality figure. It is written in R and can both run on a laptop computer
   independently or be integrated into computational workflows on a
   high-performance cluster. Releases, source code, and documentation are
   freely available at https://github.com/ulelab/clipplotr.},
Publisher = {COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT},
Address = {1 BUNGTOWN RD, COLD SPRING HARBOR, NY 11724 USA},
Type = {Article},
Language = {English},
Affiliation = {Chakrabarti, AM (Corresponding Author), Francis Crick Inst, London NW1 4AT, England.
   Chakrabarti, Anob M. M.; Capitanchik, Charlotte; Ule, Jernej; Luscombe, Nicholas M. M., Francis Crick Inst, London NW1 4AT, England.
   Ule, Jernej, Kings Coll London, UK Dementia Res Inst, Inst Psychiat Psychol \& Neurosci, London SE5 9RX, England.
   Luscombe, Nicholas M. M., Okinawa Inst Sci \& Technol Grad Univ, Onna, Okinawa 9040495, Japan.},
DOI = {10.1261/rna.079326.122},
ISSN = {1355-8382},
EISSN = {1469-9001},
Keywords = {RNA-protein interactions; CLIP technologies; data integration; data
   visualization},
Keywords-Plus = {RNA INTERACTIONS; BINDING; TRANSCRIPTOME; ROBUST},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {anob.chakrabarti@crick.ac.uk},
Affiliations = {Francis Crick Institute; University of London; King's College London;
   Okinawa Institute of Science \& Technology Graduate University},
ResearcherID-Numbers = {Luscombe, Nicholas/IXD-9918-2023
   Capitanchik, Charlotte/AAS-8464-2020
   Ule, Jernej/C-6315-2013
   },
ORCID-Numbers = {Luscombe, Nicholas/0000-0001-5293-4778
   Capitanchik, Charlotte/0000-0001-9590-2792
   Ule, Jernej/0000-0002-2452-4277
   Chakrabarti, Anob/0000-0002-6841-5718},
Funding-Acknowledgement = {Wellcome Trust {[}FC010110, 215593/Z/19/Z]; Francis Crick Institute from
   Cancer Research UK {[}FC010110]; UK Medical Research Council
   {[}FC010110]; Wellcome Trust PhD Training Fellowship for Clinicians
   Award {[}SGL023\textbackslash{}1085]; Crick Postdoctoral Clinical
   Fellowship; Academy of Medical Sciences; Okinawa Institute of Science \&
   Technology Graduate University;  {[}110292/Z/15/Z]; Wellcome Trust
   {[}215593/Z/19/Z] Funding Source: Wellcome Trust},
Funding-Text = {We would like to thank members of the Ule and Luscombe laboratories for
   testing the tool and providing user feedback during its development, in
   particular Andrea Elser, Martina Hallegger, and Flora Lee. This research
   was funded in whole or in part by the Wellcome Trust (FC010110;
   215593/Z/19/Z). For the purpose of Open Access, the author has applied a
   CC BY public copyright license to any Author Accepted Manuscript version
   arising from this submission. This work was supported by the Francis
   Crick Institute, which receives its core funding from Cancer Research UK
   (FC010110), the UK Medical Research Council (FC010110), and the Wellcome
   Trust (FC010110). A.M.C. was supported by a Wellcome Trust PhD Training
   Fellowship for Clinicians Award (110292/Z/15/Z) and is currently
   supported by a Crick Postdoctoral Clinical Fellowship and a Starter
   Grant for Clinical Lecturers from the Academy of Medical Sciences
   (SGL023\textbackslash{}1085). This work was also supported by Wellcome
   Trust Joint Investigator Awards (215593/Z/19/Z) to J.U. and N.M.L.
   N.M.L. is additionally supported by core funding from the Okinawa
   Institute of Science \& Technology Graduate University.},
Number-of-Cited-References = {28},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {RNA},
Doc-Delivery-Number = {G5GL2},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000989437200001},
OA = {Bronze, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000462587400002,
Author = {Zhang, Zhang and Zhao, Wenming and Xiao, Jingfa and Bao, Yiming and
   Wang, Fan and Hao, Lili and Zhu, Junwei and Chen, Tingting and Zhang,
   Sisi and Chen, Xu and Tang, Bixia and Zhou, Qing and Wang, Zhonghuang
   and Dong, Lili and Wang, Yanqing and Ma, Yingke and Zhang, Zhewen and
   Wang, Zhonghuang and Chen, Meili and Tian, Dongmei and Li, Cuiping and
   Teng, Xufei and Du, Zhenglin and Yuan, Na and Zeng, Jingyao and Wang,
   Jinyue and Shi, Shuo and Zhang, Yadong and Wang, Qi and Pan, Mengyu and
   Qian, Qiheng and Song, Shuhui and Niu, Guangyi and Li, Man and Xia, Lin
   and Zou, Dong and Zhang, Yuansheng and Sang, Jian and Li, Mengwei and
   Zhang, Yang and Wang, Pei and Gao, Qianwen and Liang, Fang and Li,
   Rujiao and Liu, Lin and Cao, Jiabao and abbasi, Amir A. and Shireen,
   Huma and Li, Zhao and Xiong, Zhuang and Jiang, Meiye and Guo, Tongkun
   and Li, Zhaohua and Zhang, Hao and Ma, Lina and Gao, Ran and Zhang, Tao
   and Li, Wulue and Zhang, Xiangquan and Lan, Li and Zhai, Shuang and
   Zhang, Yaping and Wang, Guodong and Wang, Zhennan and Xue, Yongbiao and
   Sun, Yubin and Yu, Lei and Sun, Mingyuan and Chen, Huanxin and Hu, Hui
   and Guo, An-Yuan and Lin, Shaofeng and Xue, Yu and Wang, Chenwei and
   Ning, Wanshan and Zhang, Ying and Luo, Hao and Gao, Feng and Guo, Yaping
   and Zhang, Qiong and Zhou, Jiaqi and Huang, Zhou and Cui, Qinghua and
   Miao, Ya-Ru and Ruan, Chen and Yuan, Chunhui and Chen, Ming and Jinpu,
   Jin and Gao, Ge and Xu, Haodong and Li, Yumei and Li, Chuan-Yun and
   Tang, Qing and Peng, Di and Deng, Wankun and Big Data Ctr Members},
Title = {Database Resources of the BIG Data Center in 2019},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2019},
Volume = {47},
Number = {D1},
Pages = {D8-D14},
Month = {JAN 8},
Abstract = {The BIG Data Center at Beijing Institute of Genomics (BIG) of the
   Chinese Academy of Sciences provides a suite of database resources in
   support of worldwide research activities in both academia and industry.
   With the vast amounts of multi-omics data generated at unprecedented
   scales and rates, the BIG Data Center is continually expanding, updating
   and enriching its core database resources through big data integration
   and value-added curation. Resources with significant updates in the past
   year include BioProject (a biological project library), BioSample (a
   biological sample library), Genome Sequence Archive (GSA, a data
   repository for archiving raw sequence reads), Genome Warehouse (GWH, a
   centralized resource housing genome-scale data), Genome Variation Map
   (GVM, a public repository of genome variations), Science Wikis (a
   catalog of biological knowledge wikis for community annotations) and
   IC4R (Information Commons for Rice). Newly released resources include
   EWAS Atlas (a knowledgebase of epigenome-wide association studies), iDog
   (an integrated omics data resource for dog) and RNA editing resources
   (for editome-disease associations and plant RNA editosome,
   respectively). To promote biodiversity and health big data sharing
   around the world, the Open Biodiversity and Health Big Data (BHBD)
   initiative is introduced. All of these resources are publicly accessible
   at http://bigd.big.ac.cn.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Zhang, Z; Zhao, WM; Xiao, JF; Bao, YM (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Zhang, Z; Zhao, WM; Xiao, JF; Bao, YM (Corresponding Author), Chinese Acad Sci, Beijing Inst Genom, Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Z; Zhao, WM; Xiao, JF; Bao, YM (Corresponding Author), Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Zhang, Z; Zhao, WM (Corresponding Author), Univ Chinese Acad Sci, Sch Future Technol, Beijing 100049, Peoples R China.
   Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Wang, Fan; Hao, Lili; Zhu, Junwei; Chen, Tingting; Zhang, Sisi; Chen, Xu; Tang, Bixia; Zhou, Qing; Wang, Zhonghuang; Dong, Lili; Wang, Yanqing; Ma, Yingke; Zhang, Zhewen; Wang, Zhonghuang; Chen, Meili; Tian, Dongmei; Li, Cuiping; Teng, Xufei; Du, Zhenglin; Yuan, Na; Zeng, Jingyao; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Wang, Qi; Pan, Mengyu; Qian, Qiheng; Song, Shuhui; Niu, Guangyi; Li, Man; Xia, Lin; Zou, Dong; Zhang, Yuansheng; Sang, Jian; Li, Mengwei; Zhang, Yang; Wang, Pei; Gao, Qianwen; Liang, Fang; Li, Rujiao; Liu, Lin; Cao, Jiabao; Li, Zhao; Xiong, Zhuang; Jiang, Meiye; Guo, Tongkun; Li, Zhaohua; Zhang, Hao; Ma, Lina; Zhang, Tao; Lan, Li; Zhai, Shuang; Sun, Yubin; Yu, Lei; Sun, Mingyuan; Chen, Huanxin, Chinese Acad Sci, Beijing Inst Genom, BIG Data Ctr, Beijing 100101, Peoples R China.
   Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Hao, Lili; Ma, Yingke; Zhang, Zhewen; Wang, Zhonghuang; Chen, Meili; Teng, Xufei; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Wang, Qi; Pan, Mengyu; Qian, Qiheng; Song, Shuhui; Niu, Guangyi; Li, Man; Xia, Lin; Zou, Dong; Zhang, Yuansheng; Sang, Jian; Li, Mengwei; Zhang, Yang; Wang, Pei; Gao, Qianwen; Li, Rujiao; Liu, Lin; Cao, Jiabao; Li, Zhao; Xiong, Zhuang; Jiang, Meiye; Guo, Tongkun; Li, Zhaohua; Zhang, Hao; Ma, Lina; Zhang, Tao, Chinese Acad Sci, Beijing Inst Genom, Key Lab Genome Sci \& Informat, Beijing 100101, Peoples R China.
   Zhang, Zhang; Zhao, Wenming; Xiao, Jingfa; Bao, Yiming; Tang, Bixia; Zhou, Qing; Wang, Zhonghuang; Teng, Xufei; Wang, Jinyue; Shi, Shuo; Zhang, Yadong; Wang, Qi; Pan, Mengyu; Qian, Qiheng; Niu, Guangyi; Li, Man; Xia, Lin; Zhang, Yuansheng; Sang, Jian; Li, Mengwei; Zhang, Yang; Wang, Pei; Gao, Qianwen; Liu, Lin; Cao, Jiabao; Li, Zhao; Xiong, Zhuang; Jiang, Meiye; Guo, Tongkun; Li, Zhaohua; Zhang, Hao; Gao, Ran; Zhang, Tao; Wang, Zhennan; Xue, Yongbiao, Univ Chinese Acad Sci, Beijing 100049, Peoples R China.
   Zhang, Zhang; Zhao, Wenming; Li, Zhaohua; Xue, Yongbiao, Univ Chinese Acad Sci, Sch Future Technol, Beijing 100049, Peoples R China.
   Gao, Ran; Xue, Yongbiao, Chinese Acad Sci, Beijing Inst Genom, Beijing, Peoples R China.
   abbasi, Amir A.; Shireen, Huma, Quaid I Azam Univ, Fac Biol Sci, Programme Comparat \& Evolutionary Genom, Natl Ctr Bioinformat, Islamabad 45320, Pakistan.
   Li, Wulue; Zhang, Xiangquan; Zhang, Yaping; Wang, Guodong; Zhang, Qiong; Xu, Haodong, Chinese Acad Sci, Kunming Inst Zool, State Key Lab Genet Resources \& Evolut, Kunming 650223, Yunnan, Peoples R China.
   Wang, Zhennan, Chinese Acad Sci, Inst Zool, State Key Lab Integrated Management Pest Insects, Beijing 100101, Peoples R China.
   Hu, Hui; Guo, An-Yuan; Lin, Shaofeng; Xue, Yu; Wang, Chenwei; Ning, Wanshan; Zhang, Ying; Guo, Yaping; Zhou, Jiaqi; Miao, Ya-Ru; Ruan, Chen; Tang, Qing; Peng, Di; Deng, Wankun, Huazhong Univ Sci \& Technol, Hubei Bioinformat \& Mol Imaging Key Lab, Dept Bioinformat \& Syst Biol, Key Lab Mol Biophys,Minist Educ,Coll Life Sci \& T, Wuhan 430074, Hubei, Peoples R China.
   Luo, Hao; Gao, Feng, Tianjin Univ, Dept Phys, Tianjin 300072, Peoples R China.
   Luo, Hao; Gao, Feng, Tianjin Univ, Key Lab Syst Bioengn, Minist Educ, Tianjin 300072, Peoples R China.
   Luo, Hao; Gao, Feng, Tianjin Univ, Collaborat Innovat Ctr Chem Sci \& Engn Tianjin, SynBio Res Platform, Tianjin 300072, Peoples R China.
   Huang, Zhou; Cui, Qinghua, Peking Univ, Sch Basic Med Sci, Dept Biomed Informat, MOE,Key Lab Cardiovasc Sci, Beijing 100191, Peoples R China.
   Yuan, Chunhui; Chen, Ming, Zhejiang Univ, Coll Life Sci, Inst Plant Sci, Dept Bioinformat,State Key Lab Plant Phys \& Bioch, Hangzhou 310058, Zhejiang, Peoples R China.
   Jinpu, Jin; Gao, Ge, Peking Univ, Ctr Bioinformat, Beijing 100871, Peoples R China.
   Li, Yumei; Li, Chuan-Yun, Peking Univ, Inst Mol Med, Beijing 100871, Peoples R China.},
DOI = {10.1093/nar/gky993},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENOME SEQUENCE; KNOWLEDGEBASE; CURATION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {zhangzhang@big.ac.cn
   zhaowm@big.ac.cn
   xiaojingfa@big.ac.cn
   baoym@big.ac.cn},
Affiliations = {Chinese Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese
   Academy of Sciences; Beijing Institute of Genomics, CAS; Chinese Academy
   of Sciences; University of Chinese Academy of Sciences, CAS; Chinese
   Academy of Sciences; University of Chinese Academy of Sciences, CAS;
   Chinese Academy of Sciences; Beijing Institute of Genomics, CAS; Quaid I
   Azam University; Chinese Academy of Sciences; Kunming Institute of
   Zoology, CAS; Chinese Academy of Sciences; Institute of Zoology, CAS;
   Huazhong University of Science \& Technology; Tianjin University;
   Tianjin University; Tianjin University; Peking University; Zhejiang
   University; Peking University; Peking University},
ResearcherID-Numbers = {Jiang, Yu/JEZ-9814-2023
   Ma, Lina/AAD-2435-2019
   song, shuhui/D-6015-2014
   Chen, Ming/AAV-3682-2020
   dong, wang/T-9093-2019
   xiong, zhuang/HTS-1094-2023
   jin, li/IWU-4648-2023
   Gao, Feng/C-9913-2009
   Qiong, Zhang/JDV-9691-2023
   Lin, Shaofeng/GWV-6464-2022
   Zhang, Yanchao/JMB-7717-2023
   zhang, zheng/HCH-9684-2022
   xiao, jing/HRB-7391-2023
   liu, xiao/JLL-2119-2023
   Deng, Wankun/HRC-3064-2023
   zhang, zhang/GQZ-6804-2022
   Zhang, Zhang/JAX-2097-2023
   tian, dongmei/HIR-8892-2022
   Huang, Zhou/D-8911-2011
   wu, yi/JEP-1581-2023
   wu, p/JDW-5015-2023
   王, 娅冰/JGE-0541-2023
   Xue, Yu/G-5929-2011
   sun, jiamin/JPY-2155-2023
   Luo, Hao/M-6339-2013
   Wang, Pei/HNR-3697-2023
   Gao, Ge/F-3615-2012
   xu, haodong/IAM-9132-2023
   Wang, Chenwei/HCI-8930-2022
   Abbasi, Amir/I-7995-2015
   wang, yanqing/C-5680-2014
   Yang, Min/JPY-3791-2023
   wang, wei/JBS-7400-2023
   Zhang, Sisi/AFV-4667-2022
   Wang, Jing/IQW-3496-2023
   Zhang, Qiong/AIC-0940-2022
   Miao, Ya-Ru/AAW-9047-2021
   Teng, Xufei/JMQ-0733-2023
   li, jiaxin/JNT-5073-2023
   },
ORCID-Numbers = {Chen, Ming/0000-0002-9677-1699
   Gao, Feng/0000-0002-9563-3841
   Lin, Shaofeng/0000-0002-1177-5480
   Deng, Wankun/0000-0002-5052-9151
   tian, dongmei/0000-0003-0564-625X
   Xue, Yu/0000-0002-9403-6869
   Luo, Hao/0000-0003-2714-8817
   Wang, Pei/0000-0002-3386-7159
   wang, yanqing/0000-0002-3054-3079
   Wang, Jing/0000-0002-8296-2961
   Zhang, Qiong/0000-0001-5001-8434
   Miao, Ya-Ru/0000-0002-1982-3141
   zhang, si si/0000-0002-3852-4796
   Guo, Tongkun/0000-0003-3397-295X
   zou, dong/0000-0002-7169-4965
   Wang, Zhennan/0000-0003-4883-2538
   Ma, Lina/0000-0001-6390-6289
   Li, Zhao/0000-0001-7374-3348
   Pan, Mengyu/0000-0002-9899-1345
   Zhang, Zhang/0000-0001-6603-5060},
Funding-Acknowledgement = {Strategic Priority Research Program of the Chinese Academy of Sciences
   (CAS) {[}XDA19050302, XDB13040500, XDA08020102]; National Key Research
   \& Development Program of China {[}2018YFC0310602, 2017YFC0907502,
   2017YFC0907503, 2017YFC0908403, 2017YFC1201200, 2016YFC0901603,
   2016YFB0201702, 2016YFC0901903, 2016YFE0206600]; National Natural
   Science Foundation of China {[}31771465, 31671360, 31571358];
   International Partnership Program of the CAS {[}153F11KYSB20160008];
   13th Five-year Informatization Plan of CAS {[}XXH13505-05]; Key Program
   of the Chinese Academy of Sciences {[}KJZD-EW-L14]; Key Technology
   Talent Program of the CAS; Youth Innovation Promotion Association of the
   CAS {[}2017141, 2018134]; Special Project on Precision Medicine under
   the National Key RD Program {[}SQ2017YFSF090210]; Open Biodiversity and
   Health Big Data Initiative of IUBS; Strategic Priority Research Program
   of the CAS {[}XDA19050302]; 100 Talent Program of the Chinese Academy of
   Sciences},
Funding-Text = {Strategic Priority Research Program of the Chinese Academy of Sciences
   (CAS) {[}XDA19050302, XDB13040500, XDA08020102]; National Key Research
   \& Development Program of China {[}2018YFC0310602, 2017YFC0907502,
   2017YFC0907503, 2017YFC0908403, 2017YFC1201200, 2016YFC0901603,
   2016YFB0201702, 2016YFC0901903, 2016YFE0206600]; National Natural
   Science Foundation of China {[}31771465, 31671360, 31571358];
   International Partnership Program of the CAS {[}153F11KYSB20160008];
   13th Five-year Informatization Plan of CAS {[}XXH13505-05]; Key Program
   of the Chinese Academy of Sciences {[}KJZD-EW-L14]; Key Technology
   Talent Program of the CAS; The 100 Talent Program of the Chinese Academy
   of Sciences; The Youth Innovation Promotion Association of the CAS
   {[}2017141, 2018134]; The Special Project on Precision Medicine under
   the National Key R\&D Program {[}SQ2017YFSF090210]; The Open
   Biodiversity and Health Big Data Initiative of IUBS. Funding for open
   access charge: Strategic Priority Research Program of the CAS
   {[}XDA19050302].},
Number-of-Cited-References = {31},
Times-Cited = {95},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {67},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {HQ7GH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000462587400002},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000551568800002,
Author = {Butchers, Joe and Williamson, Sam and Booker, Julian and Tran, Anh and
   Karki, Prem Bikram and Gautam, Biraj},
Title = {Understanding sustainable operation of micro-hydropower: a field study
   in Nepal},
Journal = {ENERGY FOR SUSTAINABLE DEVELOPMENT},
Year = {2020},
Volume = {57},
Pages = {12-21},
Month = {AUG},
Abstract = {Off-grid renewable energy technologies are important in improving
   electricity access for rural communities. However, methods for ensuring
   their sustainable operation are often poorly understood. In this
   article, existing approaches for the assessment of off-grid projects are
   examined. Reliability of the technology, financial viability and
   community engagement are identified as the 3 key areas governing the
   sustainability of projects. Focusing on these areas, a methodology is
   proposed to understand the sustainability of micro-hydropower plants. A
   mixed -methods approach including a maintenance assessment and
   interviews with managers, operators and con-sumers is used to evaluate
   24 sites in Nepal. Technically, the results of the study showed that
   trained operators delivered a higher standard of maintenance, however,
   technical issues were identified that arise during the design,
   manufacture and installation phases. The financial viability of plants
   was aided by charging consumers based on consumption, whilst plants with
   a higher rated capacity tended to benefit from a larger number of
   pro-ductive end uses. Community engagement was fostered through the
   local identity of the plant however this was threatened by societal
   changes. Inherent features of the site, such as rated power and the
   population density, in-ternal resilience to short-term shock events
   (failure of components, insufficient collection of tariffs and departure
   of trained operators) and long-term external development (increased
   incomes, increased energy consumptions and growth in rural settlements)
   were found to affect the sustainability of plants. (C) 2020 The
   Author(s). Published by Elsevier Inc. on behalf of International Energy
   Initiative. This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Butchers, J (Corresponding Author), Univ Bristol, Elect Energy Management Grp, Bristol, Avon, England.
   Butchers, Joe; Williamson, Sam; Booker, Julian, Univ Bristol, Elect Energy Management Grp, Bristol, Avon, England.
   Tran, Anh, Loughborough Univ, Sch Social Sci \& Humanities, Modern Energy Cooking Serv Programme, Loughborough, Leics, England.
   Karki, Prem Bikram; Gautam, Biraj, People Energy \& Environm Dev Assoc, Kathmandu, Nepal.},
DOI = {10.1016/j.esd.2020.04.007},
ISSN = {0973-0826},
EISSN = {2352-4669},
Keywords = {Micro-hydropower; Sustainability; Reliability; Assessment; Maintenance;
   Community},
Keywords-Plus = {RURAL ELECTRIFICATION; RENEWABLE ENERGY; POWER; RELIABILITY; TECHNOLOGY;
   ACCESS; LEVEL; GRIDS},
Research-Areas = {Science \& Technology - Other Topics; Energy \& Fuels},
Web-of-Science-Categories  = {Green \& Sustainable Science \& Technology; Energy \& Fuels},
Author-Email = {joe.butchers@bristol.ac.uk},
Affiliations = {University of Bristol; Loughborough University},
ORCID-Numbers = {Booker, Julian/0000-0002-5564-1724
   Williamson, Sam/0000-0003-2900-5967
   Butchers, Joe/0000-0002-1576-2062},
Funding-Acknowledgement = {Cabot Institute for the Environment; Engineering and Physical Sciences
   Research Council {[}188052]},
Funding-Text = {This study was funded by the Cabot Institute for the Environment, and a
   studentship from the Engineering and Physical Sciences Research Council,
   award reference 188052. Data are available at the University of Bristol
   data repository, data.bris, at
   https://doi.org/10.5523/bris.1k9cigxbcdiye22kuay4wbt5yu.},
Number-of-Cited-References = {45},
Times-Cited = {15},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Energy Sustain Dev.},
Doc-Delivery-Number = {MO5MB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000551568800002},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000367407900028,
Author = {Namburi, Devendra Kumar and Shi, Yunhua and Palmer, Kysen G. and Dennis,
   Anthony R. and Durrell, John H. and Cardwell, David A.},
Title = {An improved top seeded infiltration growth method for the fabrication of
   Y-Ba-Cu-O bulk superconductors},
Journal = {JOURNAL OF THE EUROPEAN CERAMIC SOCIETY},
Year = {2016},
Volume = {36},
Number = {3},
Pages = {615-624},
Month = {FEB},
Abstract = {Buffer-aided top seeded infiltration and growth (TSIG) with a suitable
   liquid phase reservoir has been compared with the top seeded melt growth
   (TSMG) process and applied successfully to fabricate single grain
   YBa2Cu3O7-delta (YBCO) bulk superconductors. A Yb-based liquid phase has
   been observed to yield the homogeneous, high density YBCO single grains
   by the TSIG technique. Sintering the Y2BaCuO5(Y-211) preform prior to
   TSIG has been found to be critical in retaining the shape of the sample
   during the infiltration and growth process. A number of advantages of
   the TSIG process have been demonstrated, including a dramatic reduction
   in sample shrinkage and a general improvement in bulk microstructure.
   TSIG processed samples also exhibit a fine and even distribution of
   unreacted, embedded Y-211 inclusions that play a key role in flux
   pinning in the fully processed bulk material. A YBCO sample of diameter
   25 mm fabricated by the optimised buffer-aided TSIG process was able to
   trap a field of 0.63 Tat 77K, which is the highest value of trapped
   field ever reported for a YBCO sample fabricated by the TSIG process.
   The technique reported here has the potential to improve further the
   microstructural and superconducting properties of single grain bulk
   YBCO, which enhances further the applications potential of these
   materials. (C) 2015 The Authors. Published by Elsevier Ltd. This is an
   open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Namburi, DK (Corresponding Author), Univ Cambridge, Dept Engn, Trumpington St, Cambridge CB2 1PZ, England.
   Namburi, Devendra Kumar; Shi, Yunhua; Palmer, Kysen G.; Dennis, Anthony R.; Durrell, John H.; Cardwell, David A., Univ Cambridge, Dept Engn, Cambridge CB2 1PZ, England.},
DOI = {10.1016/j.jeurceramsoc.2015.09.036},
ISSN = {0955-2219},
EISSN = {1873-619X},
Keywords = {YBCO; Infiltration and growth; Bulk superconductor; Pre-sintering;
   Buffer pellet},
Keywords-Plus = {CRITICAL-CURRENT DENSITY; LIQUID INFILTRATION; PARTICLE-SIZE; MELT
   GROWTH; MICROSTRUCTURE; YBCO; ORIGIN; FIELDS},
Research-Areas = {Materials Science},
Web-of-Science-Categories  = {Materials Science, Ceramics},
Author-Email = {dkn23@cam.ac.uk},
Affiliations = {University of Cambridge},
ResearcherID-Numbers = {SHI, YAN/HNI-1042-2023
   Namburi, Devendra Kumar/Q-2432-2016
   SHI, YH/HLG-1159-2023
   Durrell, John/A-4052-2008
   },
ORCID-Numbers = {Namburi, Devendra Kumar/0000-0003-3219-2708
   Durrell, John/0000-0003-0712-3102
   Cardwell, David/0000-0002-2020-2131},
Funding-Acknowledgement = {King Abdulaziz City for Science and Technology {[}KACST]; Engineering
   and Physical Sciences Research Council {[}EPSRC] {[}EP/K02910X/1]; EPSRC
   {[}EP/K02910X/1, EP/P00962X/1] Funding Source: UKRI; Engineering and
   Physical Sciences Research Council {[}EP/K02910X/1, EP/P00962X/1]
   Funding Source: researchfish},
Funding-Text = {This work was supported by King Abdulaziz City for Science and
   Technology {[}KACST] and the Engineering and Physical Sciences Research
   Council {[}EPSRC], grant number EP/K02910X/1. Additional data related to
   this publication is available at the University of Cambridge data
   repository {[}http://www.repository.cam.ac.uk/handle/1810/247678]. All
   other data accompanying this publication are available directly within
   the publication.},
Number-of-Cited-References = {42},
Times-Cited = {50},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {43},
Journal-ISO = {J. Eur. Ceram. Soc.},
Doc-Delivery-Number = {CZ9HF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000367407900028},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000383293400033,
Author = {Propp, Karsten and Marinescu, Monica and Auger, Daniel J. and O'Neill,
   Laura and Fotouhi, Abbas and Somasundaram, Karthik and Offer, Gregory J.
   and Minton, Geraint and Longo, Stefano and Wild, Mark and Knap, Vaclav},
Title = {Multi-temperature state-dependent equivalent circuit discharge model for
   lithium-sulfur batteries},
Journal = {JOURNAL OF POWER SOURCES},
Year = {2016},
Volume = {328},
Pages = {289-299},
Month = {OCT 1},
Abstract = {Lithium-sulfur (Li-S) batteries are described extensively in the
   literature, but existing computational models aimed at scientific
   understanding are too complex for use in applications such as battery
   management. Computationally simple models are vital for exploitation.
   This paper proposes a non-linear state-of-charge dependent Li-S
   equivalent circuit network (ECN) model for a Li-S cell under discharge.
   Li-S batteries are fundamentally different to Li-ion batteries, and
   require chemistry-specific models. A new Li-S model is obtained using a
   `behavioural' interpretation of the ECN model; as Li-S exhibits a
   `steep' open-circuit voltage (OCV) profile at high states-of-charge,
   identification methods are designed to take into account OCV changes
   during current pulses. The prediction-error minimization technique is
   used. The model is parameterized from laboratory experiments using a
   mixed-size current pulse profile at four temperatures from 10 degrees C
   to 50 degrees C, giving linearized ECN parameters for a range of
   states-of-charge, currents and temperatures. These are used to create a
   nonlinear polynomial-based battery model suitable for use in a battery
   management system. When the model is used to predict the behaviour of a
   validation data set representing an automotive NEDC driving cycle, the
   terminal voltage predictions are judged accurate with a root mean square
   error of 32 mV. (C) 2016 The Authors. Published by Elsevier B.V. This is
   an open access article under the CC BY license.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Auger, DJ (Corresponding Author), Cranfield Univ, Sch Aerosp Transport \& Mfg, Coll Rd, Cranfield MK43 0AL, Beds, England.
   Propp, Karsten; Auger, Daniel J.; Fotouhi, Abbas; Longo, Stefano; Knap, Vaclav, Cranfield Univ, Sch Aerosp Transport \& Mfg, Coll Rd, Cranfield MK43 0AL, Beds, England.
   Marinescu, Monica; Offer, Gregory J., Imperial Coll London, Dept Mech Engn, London SW7 2AZ, England.
   O'Neill, Laura; Somasundaram, Karthik; Minton, Geraint; Wild, Mark, OXIS Energy LTD, Culham Sci Ctr E1, Abingdon OX14 3DB, Oxon, England.
   Somasundaram, Karthik, Natl Univ Singapore, Dept Biomol \& Chem Engn, Singapore, Singapore.
   Knap, Vaclav, Aalborg Univ, Dept Energy Technol, Aalborg, Denmark.},
DOI = {10.1016/j.jpowsour.2016.07.090},
ISSN = {0378-7753},
EISSN = {1873-2755},
Keywords = {Lithium-sulfur battery; Parameter estimation; System identification;
   Battery model},
Keywords-Plus = {ION BATTERIES; MANAGEMENT; SHUTTLE; CELLS; PERFORMANCE; MECHANISM;
   SYSTEMS},
Research-Areas = {Chemistry; Electrochemistry; Energy \& Fuels; Materials Science},
Web-of-Science-Categories  = {Chemistry, Physical; Electrochemistry; Energy \& Fuels; Materials
   Science, Multidisciplinary},
Author-Email = {d.j.auger@cranfield.ac.uk},
Affiliations = {Cranfield University; Imperial College London; Culham Science Centre;
   National University of Singapore; Aalborg University},
ResearcherID-Numbers = {Knap, Vaclav/AAC-1127-2019
   wild, mark/O-7959-2019
   Auger, Daniel J./IQV-7547-2023
   Fotouhi, Abbas/AAJ-3150-2020
   },
ORCID-Numbers = {Knap, Vaclav/0000-0003-0108-1714
   Auger, Daniel J./0000-0002-6199-4251
   Fotouhi, Abbas/0000-0002-5402-8629
   Wild, Mark/0000-0001-6523-7277
   Somasundaram, Karthik/0000-0003-2174-8504
   Longo, Stefano/0000-0001-7874-4526
   Offer, Gregory/0000-0003-1324-8366
   Marinescu, Monica/0000-0003-1641-3371},
Funding-Acknowledgement = {Innovate UK {[}TS/L000903/1]; EPSRC {[}EP/L505286/1, EP/L505298/1];
   EPSRC {[}EP/L505286/1, EP/L505298/1] Funding Source: UKRI; Engineering
   and Physical Sciences Research Council {[}EP/L505286/1, EP/L505298/1]
   Funding Source: researchfish},
Funding-Text = {This research was undertaken as part of the Revolutionary Electric
   Vehicle Battery (REVB) project, co-funded by Innovate UK under grant
   TS/L000903/1; university funding is provided by EPSRC under grants
   number EP/L505286/1 and EP/L505298/1. The underlying data can be
   accessed through the Cranfield University data repository at
   https://dx.doLorg/10.17862/cranfield.rd.c.3292031.},
Number-of-Cited-References = {52},
Times-Cited = {54},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {93},
Journal-ISO = {J. Power Sources},
Doc-Delivery-Number = {DV9WR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000383293400033},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000796057100001,
Author = {Rafee, Ahmed and Riepenhausen, Sarah and Neuhaus, Philipp and Meidt,
   Alexandra and Dugas, Martin and Varghese, Julian},
Title = {ELaPro, a LOINC-mapped core dataset for top laboratory procedures of
   eligibility screening for clinical trials},
Journal = {BMC MEDICAL RESEARCH METHODOLOGY},
Year = {2022},
Volume = {22},
Number = {1},
Month = {MAY 14},
Abstract = {Background Screening for eligible patients continues to pose a great
   challenge for many clinical trials. This has led to a rapidly growing
   interest in standardizing computable representations of eligibility
   criteria (EC) in order to develop tools that leverage data from
   electronic health record (EHR) systems. Although laboratory procedures
   (LP) represent a common entity of EC that is readily available and
   retrievable from EHR systems, there is a lack of interoperable data
   models for this entity of EC. A public, specialized data model that
   utilizes international, widely-adopted terminology for LP, e.g. Logical
   Observation Identifiers Names and Codes (LOINC (R)), is much needed to
   support automated screening tools. Objective The aim of this study is to
   establish a core dataset for LP most frequently requested to recruit
   patients for clinical trials using LOINC terminology. Employing such a
   core dataset could enhance the interface between study feasibility
   platforms and EHR systems and significantly improve automatic patient
   recruitment. Methods We used a semi-automated approach to analyze 10,516
   screening forms from the Medical Data Models (MDM) portal's data
   repository that are pre-annotated with Unified Medical Language System
   (UMLS). An automated semantic analysis based on concept frequency is
   followed by an extensive manual expert review performed by physicians to
   analyze complex recruitment-relevant concepts not amenable to automatic
   approach. Results Based on analysis of 138,225 EC from 10,516 screening
   forms, 55 laboratory procedures represented 77.87\% of all UMLS
   laboratory concept occurrences identified in the selected EC forms. We
   identified 26,413 unique UMLS concepts from 118 UMLS semantic types and
   covered the vast majority of Medical Subject Headings (MeSH) disease
   domains. Conclusions Only a small set of common LP covers the majority
   of laboratory concepts in screening EC forms which supports the
   feasibility of establishing a focused core dataset for LP. We present
   ELaPro, a novel, LOINC-mapped, core dataset for the most frequent 55 LP
   requested in screening for clinical trials. ELaPro is available in
   multiple machine-readable data formats like CSV, ODM and HL7 FHIR. The
   extensive manual curation of this large number of free-text EC as well
   as the combining of UMLS and LOINC terminologies distinguishes this
   specialized dataset from previous relevant datasets in the literature.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Rafee, A; Varghese, J (Corresponding Author), Univ Munster, Inst Med Informat, Munster, Germany.
   Rafee, A (Corresponding Author), Univ Hosp Munster, Dept Internal Med D, Munster, Germany.
   Rafee, Ahmed; Riepenhausen, Sarah; Neuhaus, Philipp; Meidt, Alexandra; Varghese, Julian, Univ Munster, Inst Med Informat, Munster, Germany.
   Rafee, Ahmed, Univ Hosp Munster, Dept Internal Med D, Munster, Germany.
   Dugas, Martin, Heidelberg Univ Hosp, Inst Med Informat, Heidelberg, Germany.},
DOI = {10.1186/s12874-022-01611-y},
Article-Number = {141},
EISSN = {1471-2288},
Keywords = {Eligibility screening; UMLS; LOINC; Data models; Medical informatics},
Keywords-Plus = {RANDOMIZED CONTROLLED-TRIALS; PATIENT ENROLLMENT; RECRUITMENT; CRITERIA;
   RETENTION; STANDARDIZATION; REPRESENTATION; EFFICIENCY; IMPROVE; UMLS},
Research-Areas = {Health Care Sciences \& Services},
Web-of-Science-Categories  = {Health Care Sciences \& Services},
Author-Email = {ahmed.rafee@outlook.de
   julian.varghese@uni-muenster.de},
Affiliations = {University of Munster; University of Munster; Ruprecht Karls University
   Heidelberg},
ResearcherID-Numbers = {Neuhaus, Philipp/A-7758-2013
   Dugas, Martin/HLQ-6447-2023},
ORCID-Numbers = {Neuhaus, Philipp/0000-0003-1028-2884
   Dugas, Martin/0000-0001-9740-0788},
Funding-Acknowledgement = {Projekt DEAL},
Funding-Text = {Open Access funding enabled and organized by Projekt DEAL. All authors
   confirm that there is no funding to declare in this study.},
Number-of-Cited-References = {77},
Times-Cited = {3},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {7},
Journal-ISO = {BMC Med. Res. Methodol.},
Doc-Delivery-Number = {1G7UY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000796057100001},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000427197600002,
Author = {Gabdank, Idan and Chan, Esther T. and Davidson, Jean M. and Hilton,
   Jason A. and Davis, Carrie A. and Baymuradov, Ulugbek K. and Narayanan,
   Aditi and Onate, Kathrina C. and Graham, Keenan and Miyasato, Stuart R.
   and Dreszer, Timothy R. and Strattan, J. Seth and Jolanki, Otto and
   Tanaka, Forrest Y. and Hitz, Benjamin C. and Sloan, Cricket A. and
   Cherry, J. Michael},
Title = {Prevention of data duplication for high throughput sequencing
   repositories},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2018},
Month = {FEB 27},
Abstract = {Prevention of unintended duplication is one of the ongoing challenges
   many databases have to address. Working with high-throughput sequencing
   data, the complexity of that challenge increases with the complexity of
   the definition of a duplicate. In a computational data model, a data
   object represents a real entity like a reagent or a biosample. This
   representation is similar to how a card represents a book in a paper
   library catalog. Duplicated data objects not only waste storage, they
   can mislead users into assuming the model represents more than the
   single entity. Even if it is clear that two objects represent a single
   entity, data duplication opens the door to potential inconsistencies
   between the objects since the content of the duplicated objects can be
   updated independently, allowing divergence of the metadata associated
   with the objects. Analogously to a situation in which a catalog in a
   paper library would contain by mistake two cards for a single copy of a
   book. If these cards are listing simultaneously two different
   individuals as current book borrowers, it would be difficult to
   determine which borrower (out of the two listed) actually has the book.
   Unfortunately, in a large database with multiple submitters, unintended
   duplication is to be expected. In this article, we present three
   principal guidelines the Encyclopedia of DNA Elements (ENCODE) Portal
   follows in order to prevent unintended duplication of both actual files
   and data objects: definition of identifiable data objects (I), object
   uniqueness validation (II) and de-duplication mechanism (III). In
   addition to explaining our modus operandi, we elaborate on the methods
   used for identification of sequencing data files. Comparison of the
   approach taken by the ENCODE Portal vs other widely used biological data
   repositories is provided.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Cherry, JM (Corresponding Author), Stanford Univ, Dept Genet, Stanford, CA 94305 USA.
   Gabdank, Idan; Chan, Esther T.; Davidson, Jean M.; Hilton, Jason A.; Davis, Carrie A.; Baymuradov, Ulugbek K.; Narayanan, Aditi; Onate, Kathrina C.; Graham, Keenan; Miyasato, Stuart R.; Dreszer, Timothy R.; Strattan, J. Seth; Jolanki, Otto; Tanaka, Forrest Y.; Hitz, Benjamin C.; Sloan, Cricket A.; Cherry, J. Michael, Stanford Univ, Dept Genet, Stanford, CA 94305 USA.},
DOI = {10.1093/database/bay008},
Article-Number = {bay008},
ISSN = {1758-0463},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {cherry@stanford.edu},
Affiliations = {Stanford University},
ORCID-Numbers = {Chan, Esther/0000-0002-2406-2623
   Onate, M. Kathrina/0000-0003-3495-6038
   Cherry, J. Michael/0000-0001-9163-5180},
Funding-Acknowledgement = {National Human Genome Research Institute at the National Institutes of
   Health {[}U24 HG009397, U41 HG006992]; National Human Genome Research
   Institute at the United States National Institutes of Health {[}U24
   HG009397]},
Funding-Text = {National Human Genome Research Institute at the National Institutes of
   Health {[}grant numbers U24 HG009397, U41 HG006992]. The content is
   solely the responsibility of the authors and does not necessarily
   represent the official views of the National Human Genome Research
   Institute or the National Institutes of Health. The funders had no role
   in design, data processing, implementation, decision to publish or
   preparation of the manuscript. Funding for open access charge: U24 grant
   from the National Human Genome Research Institute at the United States
   National Institutes of Health {[}U24 HG009397].},
Number-of-Cited-References = {13},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Database},
Doc-Delivery-Number = {FY9PB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000427197600002},
OA = {Green Submitted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000641610200014,
Author = {Fuentes-Santos, Isabel and Labarta, Uxio and Fernandez-Reiriz, Maria
   Jose and Kay, Susan and Hjollo, Solfrid Saetre and Alvarez-Salgado, X.
   Anton},
Title = {Modeling the impact of climate change on mussel aquaculture in a coastal
   upwelling system: A critical assessment},
Journal = {SCIENCE OF THE TOTAL ENVIRONMENT},
Year = {2021},
Volume = {775},
Month = {JUN 25},
Abstract = {Forecasting of climate change impacts on marine aquaculture production
   has become a major research task, which requires taking into account the
   biases and uncertainties arising from ocean climate models in coastal
   areas, as well as considering culture management strategies. Focusing on
   the suspended mussel culture in the NW Iberian coastal upwelling system,
   we simulated current and future mussel growth by means of a
   multistructural net production Dynamic Energy Budget (DEB) model. We
   considered two scenarios and three ocean climate models to account for
   climate uncertainty, and applied a bias correction to the climate models
   in coastal areas. Our results show that the predicted impact of climate
   change on mussel growth is low compared with the role of the seeding
   time. However, the response of mussels varied across climate models,
   ranging from a minor growth decline to a moderate growth increase.
   Therefore, this work confirms that an accurate forecasting of climate
   change impacts on shellfish aquaculture should take into account the
   variability linked to both management strategies and climate
   uncertainty. (C) 2021 The Authors. Published by Elsevier B.V. This is an
   open access article under the CC BY-NC-ND license
   (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Fuentes-Santos, I (Corresponding Author), CSIC, Inst Invest Marinas IIM, C Eduardo Cabello 6, Vigo 36208, Spain.
   Fuentes-Santos, Isabel; Labarta, Uxio; Fernandez-Reiriz, Maria Jose; Alvarez-Salgado, X. Anton, CSIC, Inst Invest Marinas IIM, C Eduardo Cabello 6, Vigo 36208, Spain.
   Kay, Susan, Plymouth Marine Lab, Prospect Pl, Plymouth PL1 3DH, Devon, England.
   Hjollo, Solfrid Saetre, Inst Marine Res, Bergen, Norway.},
DOI = {10.1016/j.scitotenv.2021.145020},
EarlyAccessDate = {FEB 2021},
Article-Number = {145020},
ISSN = {0048-9697},
EISSN = {1879-1026},
Keywords = {Regional climate model; Climate uncertainty; Bias correction; Coastal
   upwelling; Management; Mytilus galloprovincialis},
Keywords-Plus = {MYTILUS-GALLOPROVINCIALIS; OCEAN ACIDIFICATION; CARBONATE SYSTEM; RAFT
   CULTURE; RESPONSES; ATLANTIC; INCREASE; QUALITY; WATERS; BUDGET},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Environmental Sciences},
Author-Email = {isafusa@iim.csic.es},
Affiliations = {Consejo Superior de Investigaciones Cientificas (CSIC); CSIC - Instituto
   de Investigaciones Marinas (IIM); Plymouth Marine Laboratory; Institute
   of Marine Research - Norway},
ResearcherID-Numbers = {Kay, Susan/C-5659-2008
   Alvarez-Salgado, Xose Anton/A-8365-2012
   },
ORCID-Numbers = {Kay, Susan/0000-0003-1510-8578
   Alvarez-Salgado, Xose Anton/0000-0002-2387-9201
   Fuentes-Santos, Isabel/0000-0002-3298-9648
   Hjollo, Solfrid Saetre/0000-0003-2897-474X},
Funding-Acknowledgement = {EU H2020 project ClimeFish {[}EU 677039]},
Funding-Text = {Field data used in this work has been provided by CSIC-PROINSA Mussel
   lab is a research laboratory jointly managed by the research group
   EsMaBa in the CSIC and PROINSA mussel farm. We wish to acknowledge the
   field work done by H. Regueiro and M. Garcia, and the contribution of
   Luis Franco to the development of the PROINSA Mussel lab data repository
   and technical support with QGIS. We also acknowledge the support of Dr.
   Jaime Otero with the NOAA SST data. This study has been funded by EU
   H2020 project ClimeFish (EU 677039).},
Number-of-Cited-References = {73},
Times-Cited = {4},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {31},
Journal-ISO = {Sci. Total Environ.},
Doc-Delivery-Number = {RP3CP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000641610200014},
OA = {hybrid, Green Accepted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000389396300009,
Author = {Carugo, Dario and Aron, Miles and Sezgin, Erdinc and de la Serna, Jorge
   Bernardino and Kuirnova, Marina K. and Eggeling, Christian and Stride,
   Eleanor},
Title = {Modulation of the molecular arrangement in artificial and biological
   membranes by phospholipid-shelled microbubbles},
Journal = {BIOMATERIALS},
Year = {2017},
Volume = {113},
Pages = {105-117},
Month = {JAN},
Abstract = {The transfer of material from phospholipid-coated microbubbles to cell
   membranes has been hypothesized to play a role in ultrasound-mediated
   drug delivery. In this study, we employed quantitative fluorescence
   microscopy techniques to investigate this phenomenon in both artificial
   and biological membrane bilayers in an acoustofluidic system. The
   results of the present study provide strong evidence for the transfer of
   material from microbubble coatings into cell membranes. Our results
   indicate that transfer of phospholipids alters the organization of
   molecules in cell membranes, specifically the lipid ordering or packing,
   which is known to be a key determinant of membrane mechanical
   properties, protein dynamics, and permeability. We further show that
   polyethylene-glycol, used in many clinical microbubble formulations,
   also has a major impact on both membrane lipid ordering and the extent
   of lipid transfer, and that this occurs even in the absence
   of,ultrasound exposure. (C) 2016 The Authors. Published by Elsevier Ltd.
   This is an open access article under the CC BY license
   (http://creativecommons.orgilicensesiby/4.0/).},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Stride, E (Corresponding Author), Univ Oxford, Inst Biomed Engn, Dept Engn Sci, Oxford OX3 7DQ, England.
   Carugo, Dario; Aron, Miles; Stride, Eleanor, Univ Oxford, Inst Biomed Engn, Dept Engn Sci, Oxford OX3 7DQ, England.
   Sezgin, Erdinc; de la Serna, Jorge Bernardino; Eggeling, Christian, Univ Oxford, Weatherall Inst Mol Med, MRC Human Immunol Unit, Headley Way, Oxford OX3 9DS, England.
   de la Serna, Jorge Bernardino, Rutherford Appleton Lab, Sci \& Technol Facil Council, Cent Laser Facil, Res Complex Harwell, Oxford OX11 0FA, England.
   Kuirnova, Marina K., Imperial Coll London, Dept Chem, London SW7 2AZ, England.
   Carugo, Dario, Univ Southampton, Engn Sci Acad Unit, Fac Engn \& Environm, Southampton SO17 1BJ, Hants, England.},
DOI = {10.1016/j.biomaterials.2016.10.034},
ISSN = {0142-9612},
EISSN = {1878-5905},
Keywords = {Microbubbles; Ultrasound; Lipid order; Membrane bilayers},
Keywords-Plus = {ULTRASOUND CONTRAST AGENTS; EFFICIENT GENE DELIVERY; MEDIATED
   DRUG-DELIVERY; ENDOTHELIAL-CELLS; LAURDAN FLUORESCENCE; COATED
   MICROBUBBLES; LIPID PACKING; SHEAR-STRESS; GENERALIZED POLARIZATION;
   FILLED MICROBUBBLES},
Research-Areas = {Engineering; Materials Science},
Web-of-Science-Categories  = {Engineering, Biomedical; Materials Science, Biomaterials},
Author-Email = {Eleanor.stride@eng.ox.ac.uk},
Affiliations = {University of Oxford; University of Oxford; UK Research \& Innovation
   (UKRI); Science \& Technology Facilities Council (STFC); STFC Rutherford
   Appleton Laboratory; Imperial College London; University of Southampton},
ResearcherID-Numbers = {Sezgin, Erdinc/R-1980-2018
   Bernardino de la Serna, Jorge/O-6355-2019
   },
ORCID-Numbers = {Sezgin, Erdinc/0000-0002-4915-388X
   Bernardino de la Serna, Jorge/0000-0002-1396-3338
   Carugo, Dario/0000-0002-1148-179X},
Funding-Acknowledgement = {Engineering and Physical Sciences Research Council (EPSRC)
   {[}EP/I021795/1, EP/I003983/1]; Marie Curie Career Integration Grant;
   Wellcome Trust {[}104924/14/Z/14]; Medical Research Council
   {[}MC\_UU\_12010, G0902418, MC\_UU\_12025]; MRC/BBSRC/ESPRC
   {[}MR/K01577X/1]; University of Oxford; BBSRC {[}BB/L014327/1] Funding
   Source: UKRI; EPSRC {[}EP/I021795/1, EP/I003983/1] Funding Source: UKRI;
   MRC {[}MC\_UU\_00008/9, MC\_UU\_12010/9, G0902418, MR/K01577X/1] Funding
   Source: UKRI; Engineering and Physical Sciences Research Council
   {[}EP/I003983/1, EP/I021795/1] Funding Source: researchfish; Medical
   Research Council {[}MC\_UU\_00008/9, G0902418, MC\_UU\_12010/9,
   MR/K01577X/1] Funding Source: researchfish},
Funding-Text = {We would like to extend our gratitude to Dr. Shamit Shrivastava for most
   helpful discussions, James Fisk and David Salisbury for the fabrication
   of the acoustofluidic devices, Dr. Joshua Owen for providing MB
   formulation protocols, and to Falk Schneider for assistance with GUV
   preparation. This work was supported financially by the Engineering and
   Physical Sciences Research Council (EPSRC EP/I021795/1). M.K.K. is
   thankful to the EPSRC for the Career Acceleration Fellowship
   (EP/I003983/1). JBdlS acknowledges support from a Marie Curie Career
   Integration Grant. CE, ES, JBdlS thank financial support by the Wellcome
   Trust (grant ref 104924/14/Z/14), the Medical Research Council (grant
   number MC\_UU\_12010/unit programmes G0902418 and MC\_UU\_12025),
   MRC/BBSRC/ESPRC (grant number MR/K01577X/1), and institutional funding
   from the University of Oxford, and the Wolfson Imaging Centre Oxford
   (Christoffer Lagerholm, Esther Garcia and Dominic Waithe) for providing
   microscope facility support and Sumita Ganguly for general lab support.
   Supporting data are available through the University of Oxford ORA data
   repository: ora.ox.ac.uk.},
Number-of-Cited-References = {76},
Times-Cited = {36},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {33},
Journal-ISO = {Biomaterials},
Doc-Delivery-Number = {EE2EK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000389396300009},
OA = {Green Published, Green Accepted, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000478611800079,
Author = {McGreevy, Paul and Masters, Sophie and Richards, Leonie and Magalhaes,
   Ricardo J. Soares and Peaston, Anne and Combs, Martin and Irwin, Peter
   J. and Lloyd, Janice and Croton, Catriona and Wylie, Claire and Wilson,
   Bethany},
Title = {Identification of Microchip Implantation Events for Dogs and Cats in the
   VetCompass Australia Database},
Journal = {ANIMALS},
Year = {2019},
Volume = {9},
Number = {7},
Month = {JUL},
Abstract = {Simple Summary The implantation of a microchip can maximise an animal's
   chance of being returned to its owners, if separated, but is also a
   statutory requirement for companion animal owners in many jurisdictions
   across Australia. This study of the electronic patient records of 1000
   randomly selected dogs and cats in the VetCompass Australia database
   revealed that the median age at microchip implantation was 74.4 days for
   individual dogs and 127.0 days for individual cats. Further exploration
   into the reasons for later microchipping in cats may be useful in
   aligning common practice with legislative requirements. In Australia,
   compulsory microchipping legislation requires that animals are
   microchipped before sale or prior to 3 months in the Australian Capital
   Territory, New South Wales, Queensland and Victoria, and by 6 months in
   Western Australia and Tasmania. Describing the implementation of
   microchipping in animals allows the data guardians to identify
   individual animals presenting to differing veterinary practices over
   their lifetimes, and to evaluate compliance with legislation. VetCompass
   Australia (VCA) collates electronic patient records from primary care
   veterinary practices into a database for epidemiological studies. VCA is
   the largest companion animal clinical data repository of its kind in
   Australia, and is therefore the ideal resource to analyse microchip data
   as a permanent unique identifier of an animal. The current study
   examined the free-text `examination record' field in the electronic
   patient records of 1000 randomly selected dogs and cats in the VCA
   database. This field may allow identification of the date of microchip
   implantation, enabling comparison with other date fields in the
   database, such as date of birth. The study revealed that the median age
   at implantation for dogs presented as individual patients, rather than
   among litters, was 74.4 days, significantly lower than for cats (127.0
   days, p = 0.003). Further exploration into reasons for later
   microchipping in cats may be useful in aligning common practice with
   legislative requirements.},
Publisher = {MDPI},
Address = {ST ALBAN-ANLAGE 66, CH-4052 BASEL, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Masters, S (Corresponding Author), Univ Sydney, Fac Sci, Sydney Sch Vet Sci, Sydney, NSW 2006, Australia.
   McGreevy, Paul; Masters, Sophie; Wylie, Claire; Wilson, Bethany, Univ Sydney, Fac Sci, Sydney Sch Vet Sci, Sydney, NSW 2006, Australia.
   Richards, Leonie, Univ Melbourne, Fac Vet \& Agr Sci, Werribee, Vic 3030, Australia.
   Magalhaes, Ricardo J. Soares; Croton, Catriona, Univ Queensland, Sch Vet Sci, Gatton, Qld 4343, Australia.
   Magalhaes, Ricardo J. Soares, Univ Queensland, Child Hlth Res Ctr, South Brisbane, Qld 4101, Australia.
   Peaston, Anne, Univ Adelaide, Sch Anim \& Vet Sci, Roseworthy, SA 5371, Australia.
   Combs, Martin, Charles Sturt Univ, Sch Anim \& Vet Sci, Sutherland Labs, Wagga Wagga, NSW 2650, Australia.
   Irwin, Peter J., Murdoch Univ, Sch Vet \& Life Sci, Murdoch, WA 6150, Australia.
   Lloyd, Janice, James Cook Univ, Coll Publ Hlth Med \& Vet Sci, Townsville, Qld 4811, Australia.},
DOI = {10.3390/ani9070423},
Article-Number = {423},
ISSN = {2076-2615},
Keywords = {cats; dogs; microchip; strays; VetCompass Australia},
Research-Areas = {Agriculture; Veterinary Sciences; Zoology},
Web-of-Science-Categories  = {Agriculture, Dairy \& Animal Science; Veterinary Sciences; Zoology},
Author-Email = {sophie.masters@sydney.edu.au},
Affiliations = {University of Sydney; University of Melbourne; University of Queensland;
   University of Queensland; University of Adelaide; Charles Sturt
   University; Murdoch University; James Cook University},
ResearcherID-Numbers = {Combs, Martin/AAV-7021-2020
   Peaston, Anne E/H-7158-2013
   Magalhaes, Ricardo J. Soares/A-5316-2010
   },
ORCID-Numbers = {Combs, Martin/0000-0003-0606-7284
   Magalhaes, Ricardo J. Soares/0000-0001-9157-8470
   Wylie, Claire/0000-0001-8076-4235
   Peaston, Anne/0000-0002-7501-2415
   McGreevy, Paul/0000-0001-7220-8378
   CROTON, Catriona/0000-0003-2179-6979
   Masters, Sophie/0000-0002-3279-2394},
Funding-Acknowledgement = {Sydney School of Veterinary Science at the University of Sydney},
Funding-Text = {The support and assistance of the heads of the Australian veterinary
   schools and the Australian Research Council are warmly acknowledged. The
   Sydney School of Veterinary Science at the University of Sydney provided
   financial support for open access publishing.},
Number-of-Cited-References = {9},
Times-Cited = {12},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Animals},
Doc-Delivery-Number = {IN3YH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000478611800079},
OA = {Green Accepted, Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000384868500013,
Author = {Jalalvand, Meisam and Czel, Gergely and Fuller, Jonathan D. and Wisnom,
   Michael R. and Canal, Luis P. and Gonzalez, Carlos D. and LLorca, Javier},
Title = {Energy dissipation during delamination in composite materials - An
   experimental assessment of the cohesive law and the stress-strain field
   ahead of a crack tip},
Journal = {COMPOSITES SCIENCE AND TECHNOLOGY},
Year = {2016},
Volume = {134},
Pages = {115-124},
Month = {OCT 6},
Abstract = {This paper presents detailed experimental information on mode-II
   delamination development in fibre/epoxy composite materials and provides
   observations about the process zone in the vicinity of the crack tip. It
   is shown that the energy dissipated in delamination propagation is spent
   on two ways (i) creating new fracture surfaces (delamination) and (ii)
   nonlinear shear deformation in the composite plies adjacent to the
   delaminating interface. Therefore, the nonlinear process zone is not
   restricted to the resin rich interface between the layers, but also
   extends into the fibre/epoxy composite layers. This is different from
   the conventional assumption in modelling delamination using cohesive
   elements where the fibre/epoxy layers are fully linear-elastic and the
   process zone is lumped at the plane of fracture. Based on the accurately
   measured displacement field around the crack tip, the experimental
   traction separation relation at the interface is found to be trapezoidal
   which is again different from the conventional bilinear cohesive law.
   (C) 2016 The Authors. Published by Elsevier Ltd. This is an open access
   article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Jalalvand, M (Corresponding Author), Univ Bristol, ACCIS, Queens Bldg,Univ Walk, Bristol BS8 1TR, Avon, England.
   Jalalvand, Meisam; Czel, Gergely; Fuller, Jonathan D.; Wisnom, Michael R., Univ Bristol, ACCIS, Queens Bldg,Univ Walk, Bristol BS8 1TR, Avon, England.
   Czel, Gergely, Budapest Univ Technol \& Econ, MTA BME Res Grp Composite Sci \& Technol, Muegyetem Rkp 3, H-1111 Budapest, Hungary.
   Canal, Luis P., Ecole Polytech Fed Lausanne, LMAF, Lausanne, Switzerland.
   Gonzalez, Carlos D.; LLorca, Javier, IMDEA Mat Inst, C Eric Kandel 2, Madrid 28906, Spain.
   Gonzalez, Carlos D.; LLorca, Javier, Univ Politecn Madrid, Dept Mat Sci, Madrid, Spain.},
DOI = {10.1016/j.compscitech.2016.08.001},
ISSN = {0266-3538},
EISSN = {1879-1050},
Keywords = {Hybrid composites; Interface; Plastic deformation; Scanning electron
   microscopy; Traction-separation law},
Keywords-Plus = {BONDED JOINTS; PSEUDO-DUCTILITY; HYBRID COMPOSITES; FRACTURE; EPOXY},
Research-Areas = {Materials Science},
Web-of-Science-Categories  = {Materials Science, Composites},
Author-Email = {m.jalalvand@bristol.ac.uk},
Affiliations = {University of Bristol; Budapest University of Technology \& Economics;
   Swiss Federal Institutes of Technology Domain; Ecole Polytechnique
   Federale de Lausanne; IMDEA Materials Institute; Universidad Politecnica
   de Madrid},
ResearcherID-Numbers = {González, Carlos/M-9897-2014
   Czél, Gergely/J-8155-2012
   González, Carlos/AAC-4265-2020
   Wisnom, Michael R./A-4413-2008
   LLorca, Javier/C-1140-2013
   },
ORCID-Numbers = {González, Carlos/0000-0002-0724-138X
   Czél, Gergely/0000-0002-6557-0886
   González, Carlos/0000-0002-0724-138X
   LLorca, Javier/0000-0002-3122-7879
   Jalalvand, Meisam/0000-0003-4691-6252},
Funding-Acknowledgement = {UK Engineering and Physical Sciences Research Council (EPSRC) Programme
   Grant {[}EP/I02946X/1]; Imperial College, London; EPSRC Building Global
   Engagements in Research grant {[}EP/K004581/1]; IMDEA Materials
   Institute; Hungarian Academy of Sciences; Janos Bolyai scholarship;
   Hungarian National Research, Development and Innovation Office - NKFIH
   {[}OTKA K 116070]; EPSRC {[}EP/K004581/1, EP/I02946X/1] Funding Source:
   UKRI; Engineering and Physical Sciences Research Council
   {[}EP/K004581/1, EP/I02946X/1] Funding Source: researchfish},
Funding-Text = {This work was funded under the UK Engineering and Physical Sciences
   Research Council (EPSRC) Programme Grant EP/I02946X/1 on High
   Performance Ductile Composite Technology in collaboration with Imperial
   College, London, and by the EPSRC Building Global Engagements in
   Research grant EP/K004581/1 in collaboration with IMDEA Materials
   Institute. Gergely Czel acknowledges the Hungarian Academy of Sciences
   for funding through the Post-Doctoral Researcher Programme fellowship
   scheme, the Janos Bolyai scholarship and the Hungarian National
   Research, Development and Innovation Office - NKFIH for funding through
   grant ref. OTKA K 116070. The authors acknowledge Hexcel Corporation for
   supplying materials for this research. Due to confidentiality agreement
   with research collaborators and industrial partners, supporting data can
   only be available to bona fide researchers subject to a non-disclosure
   agreement. Details of how to request access are available at the
   University of Bristol's data repository:
   http://doi.org/10.5523/bris.91unnvqibajq1kf7fhsat28yv.},
Number-of-Cited-References = {31},
Times-Cited = {19},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {32},
Journal-ISO = {Compos. Sci. Technol.},
Doc-Delivery-Number = {DY1QC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000384868500013},
OA = {Green Published, Green Accepted, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000434407300001,
Author = {Papp, Laszlo and Spielvogel, Clemens P. and Rausch, Ivo and Hacker,
   Marcus and Beyer, Thomas},
Title = {Personalizing Medicine Through Hybrid Imaging and Medical Big Data
   Analysis},
Journal = {FRONTIERS IN PHYSICS},
Year = {2018},
Volume = {6},
Month = {JUN 7},
Abstract = {Medical imaging has evolved from a pure visualization tool to
   representing a primary source of analytic approaches toward in vivo
   disease characterization. Hybrid imaging is an integral part of this
   approach, as it provides complementary visual and quantitative
   information in the form of morphological and functional insights into
   the living body. As such, non-invasive imaging modalities no longer
   provide images only, but data, as stated recently by pioneers in the
   field. Today, such information, together with other, non-imaging medical
   data creates highly heterogeneous data sets that underpin the concept of
   medical big data. While the exponential growth of medical big data
   challenges their processing, they inherently contain information that
   benefits a patient-centric personalized healthcare. Novel machine
   learning approaches combined with high-performance distributed cloud
   computing technologies help explore medical big data. Such exploration
   and subsequent generation of knowledge require a profound understanding
   of the technical challenges. These challenges increase in complexity
   when employing hybrid, aka dual-or even multi-modality image data as
   input to big data repositories. This paper provides a general insight
   into medical big data analysis in light of the use of hybrid imaging
   information. First, hybrid imaging is introduced (see further
   contributions to this special Research Topic), also in the context of
   medical big data, then the technological background of machine learning
   as well as state-of-the-art distributed cloud computing technologies are
   presented, followed by the discussion of data preservation and data
   sharing trends. Joint data exploration endeavors in the context of in
   vivo radiomics and hybrid imaging will be presented. Standardization
   challenges of imaging protocol, delineation, feature engineering, and
   machine learning evaluation will be detailed. Last, the paper will
   provide an outlook into the future role of hybrid imaging in view of
   personalized medicine, whereby a focus will be given to the derivation
   of prediction models as part of clinical decision support systems, to
   which machine learning approaches and hybrid imaging can be anchored.},
Publisher = {FRONTIERS MEDIA SA},
Address = {AVENUE DU TRIBUNAL FEDERAL 34, LAUSANNE, CH-1015, SWITZERLAND},
Type = {Review},
Language = {English},
Affiliation = {Beyer, T (Corresponding Author), Med Univ Vienna, QIMP Team, Ctr Med Phys \& Biomed Engn, Vienna, Austria.
   Papp, Laszlo; Rausch, Ivo; Beyer, Thomas, Med Univ Vienna, QIMP Team, Ctr Med Phys \& Biomed Engn, Vienna, Austria.
   Spielvogel, Clemens P.; Hacker, Marcus, Med Univ Vienna, Div Nucl Med, Dept Biomed Imaging \& Image Guided Therapy, Vienna, Austria.},
DOI = {10.3389/fphy.2018.00051},
Article-Number = {51},
ISSN = {2296-424X},
Keywords = {hybrid imaging; medical big data; machine learning; radiomics; holomics;
   personalized medicine},
Keywords-Plus = {POSITRON-EMISSION-TOMOGRAPHY; CELL LUNG-CANCER; TEXTURAL FEATURE
   ANALYSIS; TARGET VOLUME DEFINITION; MACHINE LEARNING-METHODS;
   SELF-ORGANIZING MAPS; PET-POSITIVE TISSUE; MARKOV RANDOM-FIELD; OPEN
   ACCESS SERIES; FDG-PET},
Research-Areas = {Physics},
Web-of-Science-Categories  = {Physics, Multidisciplinary},
Author-Email = {thomas.beyer@meduniwien.ac.at},
Affiliations = {Medical University of Vienna; Medical University of Vienna},
ResearcherID-Numbers = {Spielvogel, Clemens P./IZP-8657-2023
   Spielvogel, Clemens/IZP-8787-2023
   Hacker, Marcus/GRJ-2825-2022
   beyer, thomas/AAN-1789-2020
   Papp, Laszlo/AFT-0975-2022
   },
ORCID-Numbers = {Spielvogel, Clemens P./0000-0002-4409-8324
   Papp, Laszlo/0000-0002-9049-9989
   Rausch, Ivo/0000-0002-4007-1669},
Number-of-Cited-References = {249},
Times-Cited = {21},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {37},
Journal-ISO = {Front. Physics},
Doc-Delivery-Number = {GI5JR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000434407300001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000752406700001,
Author = {Cuellar, Luis Kuhn and Friedrich, Andreas and Gabernet, Gisela and de la
   Garza, Luis and Fillinger, Sven and Seyboldt, Adrian and Koch, Tobias
   and Zur Oven-Krockhaus, Sven and Wanke, Friederike and Richter, Sandra
   and Thaiss, Wolfgang M. and Horger, Marius and Malek, Nisar and Harter,
   Klaus and Bitzer, Michael and Nahnsen, Sven},
Title = {A data management infrastructure for the integration of imaging and
   omics data in life sciences},
Journal = {BMC BIOINFORMATICS},
Year = {2022},
Volume = {23},
Number = {1},
Month = {FEB 7},
Abstract = {Background As technical developments in omics and biomedical imaging
   increase the throughput of data generation in life sciences, the need
   for information systems capable of managing heterogeneous digital assets
   is increasing. In particular, systems supporting the findability,
   accessibility, interoperability, and reusability (FAIR) principles of
   scientific data management. Results We propose a Service Oriented
   Architecture approach for integrated management and analysis of
   multi-omics and biomedical imaging data. Our architecture introduces an
   image management system into a FAIR-supporting, web-based platform for
   omics data management. Interoperable metadata models and middleware
   components implement the required data management operations. The
   resulting architecture allows for FAIR management of omics and imaging
   data, facilitating metadata queries from software applications. The
   applicability of the proposed architecture is demonstrated using two
   technical proofs of concept and a use case, aimed at molecular plant
   biology and clinical liver cancer research, which integrate various
   imaging and omics modalities. Conclusions We describe a data management
   architecture for integrated, FAIR-supporting management of omics and
   biomedical imaging data, and exemplify its applicability for basic
   biology research and clinical studies. We anticipate that FAIR data
   management systems for multi-modal data repositories will play a pivotal
   role in data-driven research, including studies which leverage advanced
   machine learning methods, as the joint analysis of omics and imaging
   data, in conjunction with phenotypic metadata, becomes not only
   desirable but necessary to derive novel insights into biological
   processes.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Nahnsen, S (Corresponding Author), Univ Tubingen, Quantitat Biol Ctr QBiC, Tubingen, Germany.
   Nahnsen, S (Corresponding Author), Univ Tubingen, Biomed Data Sci, Dept Comp Sci, Tubingen, Germany.
   Cuellar, Luis Kuhn; Friedrich, Andreas; Gabernet, Gisela; de la Garza, Luis; Fillinger, Sven; Seyboldt, Adrian; Koch, Tobias; Nahnsen, Sven, Univ Tubingen, Quantitat Biol Ctr QBiC, Tubingen, Germany.
   Zur Oven-Krockhaus, Sven; Wanke, Friederike; Richter, Sandra; Harter, Klaus, Univ Tubingen, Ctr Plant Mol Biol ZMBP, Tubingen, Germany.
   Thaiss, Wolfgang M., Univ Tubingen, Dept Radiol Diagnost \& Intervent Radiol, Tubingen, Germany.
   Horger, Marius; Malek, Nisar; Bitzer, Michael, Univ Tubingen, Dept Internal Med 1, Tubingen, Germany.
   Nahnsen, Sven, Univ Tubingen, Biomed Data Sci, Dept Comp Sci, Tubingen, Germany.},
DOI = {10.1186/s12859-022-04584-3},
Article-Number = {61},
ISSN = {1471-2105},
Keywords = {Data integration; Imaging; Omics; Metadata models; Distributed systems;
   Service oriented architecture; Data management infrastructure},
Keywords-Plus = {PLATFORM},
Research-Areas = {Biochemistry \& Molecular Biology; Biotechnology \& Applied
   Microbiology; Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Biochemical Research Methods; Biotechnology \& Applied Microbiology;
   Mathematical \& Computational Biology},
Author-Email = {sven.nahnsen@uni-tuebingen.de},
Affiliations = {Eberhard Karls University of Tubingen; Eberhard Karls University of
   Tubingen; Eberhard Karls University of Tubingen; Eberhard Karls
   University of Tubingen; Eberhard Karls University of Tubingen},
ORCID-Numbers = {Kuhn Cuellar, Luis/0000-0002-6950-6929
   Bitzer, Michael/0000-0002-4463-8263},
Funding-Acknowledgement = {Projekt DEAL; BMBF Multiscale-HCC; DFG {[}SFB/TR 209, SFB 1101, SFB/TR
   261]; SFB 261; SFB 1101; German Ministry of Research and Education
   (BMBF) {[}01ZX1301F]; Deutsche Forschungsgemeinschaft (core facilities
   initiative) {[}KO-2313/6-1, KO-2313-2]; Deutsche Forschungsgemeinschaft
   (Institutional Strategy of the University of Tubingen) {[}ZUK 63];
   Sonderforschungsbereich SFB/TR 209 ``Liver cancer{''} of the Deutsche
   Forschungsgemeinschaft (DFG); Deutsche Forschungsgemeinschaft (DFG,
   German Research Foundation) {[}398967434-TRR 261]; Deutsche
   Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's
   Excellence Strategy-EXC {[}2124-390838134]; Deutsche
   Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's
   Excellence Strategy {[}EXC 2180-390900677]; German Ministry for
   Education and Research (BMBF, eMed/Multiscale HCC) {[}FKZ 01ZX1301A,
   01ZX1601G]},
Funding-Text = {Open Access funding enabled and organized by Projekt DEAL. Funding from
   all sources was pivotal to conduct this study. Here we outline the
   individual funding sources that contributed to the study. We acknowledge
   funding from BMBF Multiscale-HCC, DFG SFB/TR 209, DFG SFB 1101, DFG
   SFB/TR 261, Excellence cluster microbiology. S.N. and L.K.C. acknowledge
   funding from SFB 261 and FW, SzO-K. L.K.C. and K.H. acknowledge funding
   from SFB 1101 (projects D02 and Z02). G.G. acknowledges funding from the
   German Ministry of Research and Education (BMBF, Grant No. 01ZX1301F).
   S.N. acknowledges funding from Deutsche Forschungsgemeinschaft (core
   facilities initiative, KO-2313/6-1 and KO-2313-2, Institutional Strategy
   of the University of Tubingen, ZUK 63). Furthermore, S.N. acknowledges
   funding by the Sonderforschungsbereich SFB/TR 209 ``Liver cancer{''} of
   the Deutsche Forschungsgemeinschaft (DFG), as well as from the Deutsche
   Forschungsgemeinschaft (DFG, German Research Foundation)-Project-ID
   398967434-TRR 261. We acknowledge funding by the Deutsche
   Forschungsgemeinschaft (DFG, German Research Foundation) under Germany `
   s Excellence Strategy-EXC 2124-390838134 and by the Deutsche
   Forschungsgemeinschaft (DFG, German Research Foundation) under Germany's
   Excellence Strategy-EXC 2180-390900677. The clinical study (NCT02372162)
   was funded by the German Ministry for Education and Research (BMBF,
   eMed/Multiscale HCC, FKZ 01ZX1301A und 01ZX1601G, N.P.M., M.B.). Funding
   bodies did not play any role in the design of this study and in writing
   of the manuscript.},
Number-of-Cited-References = {31},
Times-Cited = {10},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {17},
Journal-ISO = {BMC Bioinformatics},
Doc-Delivery-Number = {YV0EQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000752406700001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001101596800001,
Author = {Bescond, Gael and Gales, Michele and Glineur, Regine and Sholukha,
   Viktor and Louryan, Stephane and Jan, Serge Van Sint},
Title = {Complete 3D Kinematics Parameters of the Temporo-Mandibular Joints Using
   in Vivo Data Fusion},
Journal = {IRBM},
Year = {2023},
Volume = {44},
Number = {6},
Month = {DEC},
Abstract = {Objectives: The temporo-mandibular joint (TMJ) has implications in vital
   functions and its disorder prevalence is between 5\% and 12\%. The
   mandible motions rely on two joints where mandibular condyles are
   generally asymmetric and highly individual. They rotate during jaw
   opening and closing and translate vertically and anteroposteriorly.
   Quantitative motion analysis tools are of interest to better understand
   normal and abnormal TMJ behavior. Previous studies have reported the
   asymmetrical behavior of the mandible compared to the skull as well as
   the synchronism of rotation and translation during its motions. But none
   of them has developed an experimental protocol using in vivo motion data
   fused with a tridimensional (3D) model. Therefore, we aim to provide the
   detailed kinematic parameters of the mandible compared to the skull, of
   the 2 condyles compared to their sockets and the instantaneous
   helicoidal axis (IHA) calculation through a clearly described new
   technology: in vivo data motion fused with virtual palpation on 3D
   models. We also compare the accuracy and the consistency of our results
   with the existing literature.Material and methods: Five healthy subjects
   fitted with a tailor-made dental and head clusters performed mouth
   opening/closing, diduction and chewing motions. 15 anatomical landmarks
   (ALs) were palpated on their skull and their mandible. The trajectory of
   the markers and ALs was recorded by opto-electronic cameras. 3D models
   created from magnetic resonance imaging (MRI) from the 5 subjects were
   processed through a segmentation procedure and imported into a
   musculo-skeletal data processing software. Virtual palpation was used to
   locate specific ALs and to build coordinate systems following the ISB
   recommendations. The ALs coordinates, the motion files and the
   morphological model were fused. Motion cycles were normalized from 1 to
   100\% of rotations and translations duration in coordinate systems,
   instantaneous helical axis (IHA) parameters were computed for the 3
   motions.Results: Median RMSE between manually and virtually palpated ALs
   was 8,0 mm. During opening motion, rotation around the Z-axis (median
   24,9 degrees), translations along the X-axis and the Y-axis (median 9,7
   mm and 6,3 mm respectively) were happening all at once. The IHA was
   obliquely orientated. During diduction motion, rotations around the
   Y-axis and the X-axis (median 10,7 degrees and 3.3 degrees
   respectively), translation on the Z-axis is (median -9.4 mm) occurred
   simultaneously. The IHA orientation was oblique and changed accordingly
   to the diduction side. During chewing motion, median rotation around the
   Z-axis was -2.2 degrees and median translation on the Y-axis -1.0 mm.
   The IHA pathway high asymmetry coincided with typical movements of
   working and balancing condyles. Conclusion: Complete 3D kinematics
   parameters of the TMJs, corresponding to the ISB recommendations, have
   been extracted with our methodology. Our values matched previous studies
   if available and the palpation RMSE was within the bounds of precedent
   experimental protocol. It is therefore efficient to study in vivo
   motion. Motion data have been registered in an open access data
   repository, allowing other researchers to exploit them and develop their
   own TMJ model.(c) 2023 AGBM. Published by Elsevier Masson SAS. All
   rights reserved.},
Publisher = {ELSEVIER SCIENCE INC},
Address = {STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA},
Type = {Article},
Language = {English},
Affiliation = {Bescond, G (Corresponding Author), Univ Libre Bruxelles, Fac Med, Lab Anat Biomech \& Organogenesis LABO, CP 619,Lennik St 808, B-1070 Brussels, Belgium.
   Bescond, Gael; Gales, Michele; Sholukha, Viktor; Louryan, Stephane; Jan, Serge Van Sint, Univ Libre Bruxelles, Fac Med, Lab Anat Biomech \& Organogenesis LABO, Brussels, Belgium.
   Bescond, Gael; Jan, Serge Van Sint, Univ Libre Bruxelles, Erasme Hosp, Fac Med, Ctr Funct Evaluat CFE, Brussels, Belgium.
   Gales, Michele; Glineur, Regine, Univ Libre Bruxelles, Fac Med, Dept Dent Oral \& Maxillo Facial Surg Orthodendistr, Brussels, Belgium.
   Louryan, Stephane, Univ Libre Bruxelles, Erasme Hosp, Dept Radiol, Brussels, Belgium.
   Bescond, Gael, Univ Libre Bruxelles, Fac Med, Lab Anat Biomech \& Organogenesis LABO, CP 619,Lennik St 808, B-1070 Brussels, Belgium.},
DOI = {10.1016/j.irbm.2023.100804},
EarlyAccessDate = {OCT 2023},
Article-Number = {100804},
ISSN = {1959-0318},
EISSN = {1876-0988},
Keywords = {Temporo-mandibular kinematics; Temporo-mandibular joints; Anatomical
   landmarks; Anatomical frames; Virtual palpation; Instantaneous helical
   axis},
Keywords-Plus = {HELICAL AXIS PATHWAYS; MOVEMENTS},
Research-Areas = {Engineering},
Web-of-Science-Categories  = {Engineering, Biomedical},
Author-Email = {gael.bescond@ulb.be},
Affiliations = {Universite Libre de Bruxelles; Universite Libre de Bruxelles; Universite
   Libre de Bruxelles; Universite Libre de Bruxelles; Universite Libre de
   Bruxelles},
Number-of-Cited-References = {34},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {IRBM},
Doc-Delivery-Number = {X9LZ7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001101596800001},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000826506100001,
Author = {Koelzsch, Andrea and Davidson, Sarah C. and Gauggel, Dominik and Hahn,
   Clemens and Hirt, Julian and Kays, Roland and Lang, Ilona and Lohr,
   Ashley and Russell, Benedict and Scharf, Anne K. and Schneider, Gabriel
   and Vinciguerra, Candace M. and Wikelski, Martin and Safi, Kamran},
Title = {MoveApps: a serverless no-code analysis platform for animal tracking
   data},
Journal = {MOVEMENT ECOLOGY},
Year = {2022},
Volume = {10},
Number = {1},
Month = {JUL 18},
Abstract = {Background Bio-logging and animal tracking datasets continuously grow in
   volume and complexity, documenting animal behaviour and ecology in
   unprecedented extent and detail, but greatly increasing the challenge of
   extracting knowledge from the data obtained. A large variety of analysis
   methods are being developed, many of which in effect are inaccessible to
   potential users, because they remain unpublished, depend on proprietary
   software or require significant coding skills. Results We developed
   MoveApps, an open analysis platform for animal tracking data, to make
   sophisticated analytical tools accessible to a global community of
   movement ecologists and wildlife managers. As part of the Movebank
   ecosystem, MoveApps allows users to design and share workflows composed
   of analysis modules (Apps) that access and analyse tracking data. Users
   browse Apps, build workflows, customise parameters, execute analyses and
   access results through an intuitive web-based interface. Apps, coded in
   R or other programming languages, have been developed by the MoveApps
   team and can be contributed by anyone developing analysis code. They
   become available to all user of the platform. To allow long-term and
   cross-system reproducibility, Apps have public source code and are
   compiled and run in Docker containers that form the basis of a
   serverless cloud computing system. To support reproducible science and
   help contributors document and benefit from their efforts, workflows of
   Apps can be shared, published and archived with DOIs in the Movebank
   Data Repository. The platform was beta launched in spring 2021 and
   currently contains 49 Apps that are used by 316 registered users. We
   illustrate its use through two workflows that (1) provide a daily report
   on active tag deployments and (2) segment and map migratory movements.
   Conclusions The MoveApps platform is meant to empower the community to
   supply, exchange and use analysis code in an intuitive environment that
   allows fast and traceable results and feedback. By bringing together
   analytical experts developing movement analysis methods and code with
   those in need of tools to explore, answer questions and inform decisions
   based on data they collect, we intend to increase the pace of knowledge
   generation and integration to match the huge growth rate in bio-logging
   data acquisition.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Kölzsch, A (Corresponding Author), Max Planck Inst Anim Behav, Dept Migrat, Obstberg 1, D-78315 Radolfzell am Bodensee, Germany.
   Kölzsch, A (Corresponding Author), Univ Konstanz, Dept Biol, Constance, Germany.
   Koelzsch, Andrea; Davidson, Sarah C.; Scharf, Anne K.; Vinciguerra, Candace M.; Wikelski, Martin; Safi, Kamran, Max Planck Inst Anim Behav, Dept Migrat, Obstberg 1, D-78315 Radolfzell am Bodensee, Germany.
   Koelzsch, Andrea; Davidson, Sarah C.; Scharf, Anne K.; Wikelski, Martin; Safi, Kamran, Univ Konstanz, Dept Biol, Constance, Germany.
   Davidson, Sarah C., Ohio State Univ, Dept Civil Environm \& Geodet Engn, Columbus, OH 43210 USA.
   Davidson, Sarah C.; Wikelski, Martin, Univ Konstanz, Ctr Adv Study Collect Behav, Constance, Germany.
   Gauggel, Dominik; Hahn, Clemens; Hirt, Julian; Russell, Benedict, Couchbits GmbH, Constance, Germany.
   Kays, Roland; Lohr, Ashley; Vinciguerra, Candace M., North Carolina Museum Nat Sci, Raleigh, NC USA.
   Kays, Roland, North Carolina State Univ, Dept Forestry \& Environm Resources, Raleigh, NC USA.
   Lang, Ilona; Schneider, Gabriel, Univ Konstanz, Commun Informat Media Ctr, Constance, Germany.},
DOI = {10.1186/s40462-022-00327-4},
Article-Number = {30},
ISSN = {2051-3933},
Keywords = {Animal movement; Movement ecology; Bio-logging; Method sharing;
   Community empowerment; Analysis code publication; Reproducibility; Cloud
   infrastructure; Serverless computing},
Keywords-Plus = {MOVEMENT; CHALLENGES; SOFTWARE; ECOLOGY; DOCKER},
Research-Areas = {Environmental Sciences \& Ecology},
Web-of-Science-Categories  = {Ecology},
Author-Email = {akoelzsch@ab.mpg.de},
Affiliations = {Max Planck Society; University of Konstanz; University System of Ohio;
   Ohio State University; University of Konstanz; North Carolina State
   University; University of Konstanz},
ResearcherID-Numbers = {Safi, Kamran/B-2079-2008
   },
ORCID-Numbers = {Safi, Kamran/0000-0002-8418-6759
   Schneider, Gabriel/0000-0001-6573-3115
   Kays, Roland/0000-0002-2947-6665
   Vinciguerra, Nix/0000-0002-2867-4491},
Funding-Acknowledgement = {Ministry for Science, Research and the Arts of Baden-Wurttemberg;
   Knobloch Family Foundation},
Funding-Text = {Open Access funding enabled and organized by Projekt DEAL. The initial
   development of MoveApps was funded by the Ministry for Science, Research
   and the Arts of Baden-Wurttemberg and the Knobloch Family Foundation.},
Number-of-Cited-References = {48},
Times-Cited = {4},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {11},
Journal-ISO = {Mov. Ecol.},
Doc-Delivery-Number = {2Z3TZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000826506100001},
OA = {gold, Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000378192200031,
Author = {Peel, Andrew J. and Slaughter, Jonathan and Wheatley, Andrew E. H.},
Title = {New options in directed cupration: Studies in heteroleptic bis(amido)
   cuprate formation},
Journal = {JOURNAL OF ORGANOMETALLIC CHEMISTRY},
Year = {2016},
Volume = {812},
Number = {SI},
Pages = {259-267},
Month = {JUN 15},
Abstract = {The 2:1 combination of MPLi (MP = 2-methylpiperidide) with CuBr gives
   the novel complex {[}(MP)(2)CuLi(THF)(2)](2)LiBr 12 and introduces the
   chiral ligand MP to the evolving field of Directed ortho Cupration
   reagents. Subsequent syntheses have focused on developing heteroleptic
   bis(amido) arrangements at Cu, with 1:1 mixtures of two out of MPLi,
   DMPLi and TMPLi (DMP = 2,6-cis-dimethylpiperidide; TMP =
   2,2,6,6-tetramethylpiperidide) being reacted with Cu-I salts in the
   presence of THF. Resulting lithiocuprates reveal solid state dimers
   based on the heteroleptic bis(amido) formulations
   R2N(TMP)Cu(Br)Li-2(THF)(2) (R2N = MP 13; R2N = DMP 14). The heteroleptic
   Gilman lithiocuprate PIP(TMP) CuLi (PIP = piperidide) 15 has also been
   prepared. In each of 12-15, significant variations in the orientations
   of the amide ligands can be rationalized in terms of steric effects and,
   in the case of 15, stabilization of the alkali metal by Me ... Li
   interaction is evidenced. (C) 2015 The Authors. Published by Elsevier
   B.V. This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER SCIENCE SA},
Address = {PO BOX 564, 1001 LAUSANNE, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Wheatley, AEH (Corresponding Author), Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England.
   Peel, Andrew J.; Slaughter, Jonathan; Wheatley, Andrew E. H., Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England.},
DOI = {10.1016/j.jorganchem.2015.09.038},
ISSN = {0022-328X},
EISSN = {1872-8561},
Keywords = {Amide ligand; Cuprate; Lithium; Structure; X-ray crystallography},
Keywords-Plus = {HIGHER-ORDER CYANOCUPRATE; MIXED AGGREGATE MAA; MEDIATED ZINCATION;
   METALATION REACTIONS; CRYSTAL-STRUCTURES; SINGLE CONCEPT; CYANO LIGAND;
   TMP-ZINCATE; LITHIUM; CHEMISTRY},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Inorganic \& Nuclear; Chemistry, Organic},
Author-Email = {aehw2@cam.ac.uk},
Affiliations = {University of Cambridge},
ORCID-Numbers = {Peel, Andrew/0000-0003-4690-5019
   Slaughter, Jonathan/0000-0002-6401-8547},
Funding-Acknowledgement = {U.K. EPSRC {[}EP/J500380/1]; EPSRC {[}EP/K039520/1] Funding Source:
   UKRI; Engineering and Physical Sciences Research Council
   {[}EP/K039520/1] Funding Source: researchfish},
Funding-Text = {This work was supported by the U.K. EPSRC through grant EP/J500380/1 (A
   P.). Thanks go to Dr. John Davies for collecting crystallographic data
   for 12 and 13, Professor Paul Raithby (Bath) for help with
   crystallographic analysis and also Mr. Duncan Howe for help with
   acquisition of <SUP>1</SUP>H,<SUP>7</SUP>Li-HOESY NMR data. A.W. also
   wishes to thank the GB Sasakawa Foundation for supporting collaboration
   with Professor Masanobu Uchiyama (Tokyo), who we thank for constructive
   discussions. Detailed supporting data for this paper are available at
   the https://www.repository.cam.ac.uk/handle/1810/251198 data repository.
   These include some data in the file formats fid (NMR spectroscopic data)
   and cif (crystallographic data), which can be opened using the programs
   TopSpin 3.2 (or similar) and Mercury CSD 3.5 (or similar), respectively.},
Number-of-Cited-References = {73},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {10},
Journal-ISO = {J. Organomet. Chem.},
Doc-Delivery-Number = {DP0PR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000378192200031},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000310270300021,
Author = {Squires, R. Burke and Noronha, Jyothi and Hunt, Victoria and
   Garcia-Sastre, Adolfo and Macken, Catherine and Baumgarth, Nicole and
   Suarez, David and Pickett, Brett E. and Zhang, Yun and Larsen,
   Christopher N. and Ramsey, Alvin and Zhou, Liwei and Zaremba, Sam and
   Kumar, Sanjeev and Deitrich, Jon and Klem, Edward and Scheuermann,
   Richard H.},
Title = {Influenza Research Database: an integrated bioinformatics resource for
   influenza research and surveillance},
Journal = {INFLUENZA AND OTHER RESPIRATORY VIRUSES},
Year = {2012},
Volume = {6},
Number = {6},
Pages = {404-416},
Month = {NOV},
Abstract = {Background The recent emergence of the 2009 pandemic influenza A/H1N1
   virus has highlighted the value of free and open access to influenza
   virus genome sequence data integrated with information about other
   important virus characteristics. sign The Influenza Research Database
   (IRD, http://www.fludb.org) is a free, open, publicly-accessible
   resource funded by the U.S. National Institute of Allergy and Infectious
   Diseases through the Bioinformatics Resource Centers program. IRD
   provides a comprehensive, integrated database and analysis resource for
   influenza sequence, surveillance, and research data, including
   user-friendly interfaces for data retrieval, visualization and
   comparative genomics analysis, together with personal log in-protected
   workbench spaces for saving data sets and analysis results. IRD
   integrates genomic, proteomic, immune epitope, and surveillance data
   from a variety of sources, including public databases, computational
   algorithms, external research groups, and the scientific literature.
   Results To demonstrate the utility of the data and analysis tools
   available in IRD, two scientific use cases are presented. A comparison
   of hemagglutinin sequence conservation and epitope coverage information
   revealed highly conserved protein regions that can be recognized by the
   human adaptive immune system as possible targets for inducing
   cross-protective immunity. Phylogenetic and geospatial analysis of
   sequences from wild bird surveillance samples revealed a possible
   evolutionary connection between influenza virus from Delaware Bay
   shorebirds and Alberta ducks.
   Conclusions The IRD provides a wealth of integrated data and information
   about influenza virus to support research of the genetic determinants
   dictating virus pathogenicity, host range restriction and transmission,
   and to facilitate development of vaccines, diagnostics, and
   therapeutics.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Scheuermann, RH (Corresponding Author), Univ Texas SW Med Ctr Dallas, Dept Pathol, 5323 Harry Hines Blvd, Dallas, TX 75390 USA.
   Squires, R. Burke; Noronha, Jyothi; Hunt, Victoria; Pickett, Brett E.; Zhang, Yun; Scheuermann, Richard H., Univ Texas SW Med Ctr Dallas, Dept Pathol, Dallas, TX 75390 USA.
   Garcia-Sastre, Adolfo, Mt Sinai Sch Med, Dept Microbiol, New York, NY USA.
   Garcia-Sastre, Adolfo, Mt Sinai Sch Med, Dept Med, Div Infect Dis, New York, NY USA.
   Garcia-Sastre, Adolfo, Mt Sinai Sch Med, Global Hlth \& Emerging Pathogens Inst, New York, NY USA.
   Macken, Catherine, Los Alamos Natl Lab, Los Alamos, NM USA.
   Baumgarth, Nicole, Univ Calif Davis, Ctr Comparat Med, Davis, CA 95616 USA.
   Suarez, David, USDA, SE Poultry Res Lab, Athens, GA USA.
   Larsen, Christopher N.; Ramsey, Alvin, Vecna Technol, Greenbelt, MD USA.
   Zhou, Liwei; Zaremba, Sam; Kumar, Sanjeev; Deitrich, Jon; Klem, Edward, Hlth IT Syst, Northrop Grumman Informat Syst, Rockville, MD USA.
   Scheuermann, Richard H., Univ Texas SW Med Ctr Dallas, Div Biomed Informat, Dallas, TX 75390 USA.},
DOI = {10.1111/j.1750-2659.2011.00331.x},
ISSN = {1750-2640},
EISSN = {1750-2659},
Keywords = {Bioinformatics; epitope; influenza virus; integrated; surveillance},
Keywords-Plus = {MULTIPLE SEQUENCE ALIGNMENT; A VIRUS; EPITOPE; MORTALITY; ANTIBODY;
   INFECTION},
Research-Areas = {Infectious Diseases; Virology},
Web-of-Science-Categories  = {Infectious Diseases; Virology},
Author-Email = {richard.scheuermann@utsouthwestern.edu},
Affiliations = {University of Texas System; University of Texas Southwestern Medical
   Center Dallas; Icahn School of Medicine at Mount Sinai; Icahn School of
   Medicine at Mount Sinai; Icahn School of Medicine at Mount Sinai; United
   States Department of Energy (DOE); Los Alamos National Laboratory;
   University of California System; University of California Davis; United
   States Department of Agriculture (USDA); University of Texas System;
   University of Texas Southwestern Medical Center Dallas},
ResearcherID-Numbers = {Pickett, Brett/AAE-3582-2020
   Baumgarth, Nicole/AAI-6949-2020
   Garcia-Sastre, Adolfo/ABF-3070-2021
   Squires, R Burke/A-7163-2008
   },
ORCID-Numbers = {Pickett, Brett/0000-0001-7930-8160
   Squires, R Burke/0000-0001-9666-6285
   Suarez, David/0000-0003-4582-6116
   Garcia-Sastre, Adolfo/0000-0002-6551-1827
   Larsen, Christopher N/0000-0002-1051-5767
   Scheuermann, Richard H./0000-0003-1355-892X
   Zhang, Yun/0000-0002-1180-275X},
Funding-Acknowledgement = {NIAID},
Funding-Text = {First and foremost, we would like to acknowledge the contribution of all
   providers of data to public database resources like GenBank and IRD.
   Without their efforts to generate the data and their willingness to make
   it freely available through public data repositories, the potential for
   the kind of comprehensive integrative data analysis illustrated here
   would not be possible. We have especially benefitted from collaborating
   with the NIAID-funded Centers of Excellence for Influenza Research and
   Surveillance (CEIRS) who have been extremely helpful in developing data
   standards, identifying use cases, and sharing their data. We also
   acknowledge the generous support received from the NIAID - N01AI40041.},
Number-of-Cited-References = {47},
Times-Cited = {231},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {52},
Journal-ISO = {Influenza Other Respir. Viruses},
Doc-Delivery-Number = {026IY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000310270300021},
OA = {hybrid, Green Published, Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000459253300001,
Author = {Maier, Christian and Christoph, Jan and Schmidt, Danilo and Ganslandt,
   Thomas and Prokosch, H. U. and Kraus, Stefan and Sedlmayr, Martin},
Title = {Experiences of Transforming a Complex Nephrologic Care and Research
   Database into i2b2 Using the IDRT Tools},
Journal = {JOURNAL OF HEALTHCARE ENGINEERING},
Year = {2019},
Volume = {2019},
Abstract = {The secondary use of data from electronic medical records has become an
   important factor to determine and to identify various causes of disease.
   For this reason, applications like informatics for integrating biology
   and the bedside (i2b2) offer a GUI-based front end to select patient
   cohorts. To make use of those tools, however, clinical data need to be
   extracted from the Electronic Health Record (EHR) system and integrated
   into the data schema of i2b2. We used TBase, a documentation system for
   nephrologic transplantations, as a source system and applied the
   Integrated Data Repository Toolkit (IDRT) for the Extract, Transform,
   and Load (ETL) process to load the data into i2b2. Since i2b2 uses an
   entity-attribute-value (EAV) schema, which is a fundamentally different
   way of modeling data in comparison to a standard relational schema in
   TBase, we evaluated if (a) the data relationship of the source system
   entities can still be represented in the i2b2 schema and if (b) the IDRT
   is a suitable solution for loading the data of a comprehensive data
   schema like TBase into i2b2. For that reason, we identified entities in
   the TBase data schema which were relevant for answering questions on
   cohort identification. By doing so, we found out that the entities had
   different structures that needed to be handled differently for the ETL
   process. Furthermore, the use of IDRT revealed shortcomings with regard
   to large input data and specific data structures that are part of most
   modern EHR systems. However, this project also showed that our way of
   modeling the TBase data in i2b2 has been proven to be successful in
   terms of answering the most common questions of clinicians on cohort
   identification.},
Publisher = {HINDAWI LTD},
Address = {ADAM HOUSE, 3RD FLR, 1 FITZROY SQ, LONDON, W1T 5HF, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Maier, C (Corresponding Author), Friedrich Alexander Univ Erlangen Nurnberg, Chair Med Informat, Erlangen, Germany.
   Maier, Christian; Christoph, Jan; Ganslandt, Thomas; Prokosch, H. U.; Kraus, Stefan; Sedlmayr, Martin, Friedrich Alexander Univ Erlangen Nurnberg, Chair Med Informat, Erlangen, Germany.
   Schmidt, Danilo, Charite Univ Med Berlin, Med Klin Nephrol, D-10117 Berlin, Germany.},
DOI = {10.1155/2019/5640685},
Article-Number = {5640685},
ISSN = {2040-2295},
EISSN = {2040-2309},
Keywords-Plus = {INFORMATICS; RECORD},
Research-Areas = {Health Care Sciences \& Services},
Web-of-Science-Categories  = {Health Care Sciences \& Services},
Author-Email = {chris.maier@fau.de},
Affiliations = {University of Erlangen Nuremberg; Free University of Berlin; Humboldt
   University of Berlin; Charite Universitatsmedizin Berlin},
ResearcherID-Numbers = {Sedlmayr, Martin/D-8828-2011
   Kraus, Stefan/X-5082-2019
   Ganslandt, Thomas/AAC-6690-2019
   },
ORCID-Numbers = {Sedlmayr, Martin/0000-0002-9888-8460
   Kraus, Stefan/0000-0001-8465-7103
   Ganslandt, Thomas/0000-0001-6864-8936
   Schmidt, Danilo/0000-0001-5236-2749},
Funding-Acknowledgement = {German Federal Ministry of Economic Affairs and Energy (BMWi); Smart
   Data Initiative {[}FKZ 01MT14001E]; Deutsche Forschungsgemeinschaft;
   Friedrich-Alexander-Universitat Erlangen-Nurnberg (FAU)},
Funding-Text = {The research was supported by the German Federal Ministry of Economic
   Affairs and Energy (BMWi) in the context of the project ``Clinical Data
   Intelligence{''} and the Smart Data Initiative (FKZ 01MT14001E). The
   authors acknowledge support of Deutsche Forschungsgemeinschaft and
   Friedrich-Alexander-Universitat Erlangen-Nurnberg (FAU) within the
   funding programme ``Open Access Publishing.{''} The authors thank
   Stephanie Newe for the linguistic proof-reading of the manuscript. The
   present work was performed in fulfillment of the requirements for
   obtaining the degree ``Dr. rer. biol. hum.{''} from the
   Friedrich-Alexander-Universitat Erlangen-Nurnberg.},
Number-of-Cited-References = {17},
Times-Cited = {5},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {12},
Journal-ISO = {J. Healthc. Eng.},
Doc-Delivery-Number = {HM1YX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000459253300001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000767931100002,
Author = {Dam, Thu A. and Forse, Rachel J. and Tran, Phuong M. T. and Vo, Luan N.
   Q. and Codlin, Andrew J. and Nguyen, Lan P. and Creswell, Jacob},
Title = {What makes community health worker models for tuberculosis active case
   finding work? A cross-sectional study of TB REACH projects to identify
   success factors for increasing case notifications},
Journal = {HUMAN RESOURCES FOR HEALTH},
Year = {2022},
Volume = {20},
Number = {1},
Month = {MAR 12},
Abstract = {Background In the field of tuberculosis (TB), Community Healthcare
   Workers (CHWs) have been engaged for advocacy, case detection, and
   patient support in a wide range of settings. Estimates predict
   large-scale shortfalls of healthcare workers in low- and middle-income
   settings by 2030 and strategies are needed to optimize the health
   workforce to achieve universal availability and accessibility of
   healthcare. In 2018, the World Health Organization (WHO) published
   guidelines on best practices for CHW engagement, and identified
   remaining knowledge gaps. Stop TB Partnership's TB REACH initiative has
   supported interventions using CHWs to deliver TB care in over 30
   countries, and utilized the same primary indicator to measure project
   impact at the population-level for all TB active case finding projects,
   which makes the results comparable across multiple settings. This study
   compiled 10 years of implementation data from the initiative's grantee
   network to begin to address key knowledge gaps in CHW networks. Methods
   We conducted a cross-sectional study analyzing the TB REACH data
   repository (n = 123) and primary survey responses (n = 50) of project
   implementers. We designed a survey based on WHO guidelines to understand
   projects' practices on CHW recruitment, training, activities,
   supervision, compensation, and sustainability. We segmented projects by
   TB notification impact and fitted linear random-effect regression models
   to identify practices associated with higher changes in notifications.
   Results Most projects employed CHWs for advocacy alongside case finding
   and holding activities. Model characteristics associated with higher
   project impact included incorporating e-learning in training and having
   the prospect of CHWs continuing their responsibilities at the close of a
   project. Factors that trended towards being associated with higher
   impact were community-based training, differentiated contracts, and
   non-monetary incentives. Conclusion In line with WHO guidelines, our
   findings emphasize that successful implementation approaches provide
   CHWs with comprehensive training, continuous supervision, fair
   compensation, and are integrated within the existing primary healthcare
   system. However, we encountered a great degree of heterogeneity in CHW
   engagement models, resulting in few practices clearly associated with
   higher notifications.},
Publisher = {BMC},
Address = {CAMPUS, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Forse, RJ (Corresponding Author), Friends Int TB Relief, 1-21 Luong St,Nhan Chinh Ward, Hanoi, Vietnam.
   Dam, Thu A.; Forse, Rachel J.; Tran, Phuong M. T.; Vo, Luan N. Q.; Codlin, Andrew J., Friends Int TB Relief, 1-21 Luong St,Nhan Chinh Ward, Hanoi, Vietnam.
   Forse, Rachel J., WHO, Collaborat Ctr TB \& Social Med, Karolinska Inst, Dept Global Publ Hlth, Solnavagen 1, S-17177 Solna, Sweden.
   Vo, Luan N. Q., IRD VN, 68B Nguyen Troi,Ward 8,Phu, Ho Chi Minh City, Vietnam.
   Nguyen, Lan P., Ctr Dev Community Hlth Initiat, 1-21 Luong St,Nhan Chin Ward, Hanoi, Vietnam.
   Creswell, Jacob, Stop TB Partnership, Chemin Pommier 40, CH-1218 Geneva, Switzerland.},
DOI = {10.1186/s12960-022-00708-1},
Article-Number = {25},
EISSN = {1478-4491},
Keywords = {Tuberculosis; Community healthcare workers; TB REACH; Impact evaluation;
   Active case finding},
Keywords-Plus = {MIDDLE-INCOME COUNTRIES; PERFORMANCE},
Research-Areas = {Health Care Sciences \& Services; Business \& Economics},
Web-of-Science-Categories  = {Health Policy \& Services; Industrial Relations \& Labor},
Author-Email = {rachel.forse@tbhelp.org},
Affiliations = {World Health Organization; Karolinska Institutet},
ResearcherID-Numbers = {Nguyen, Lan/HTL-4253-2023},
Funding-Acknowledgement = {Karolinska Institute; Global Affairs Canada {[}CA-3-D000920001]},
Funding-Text = {Open access funding provided by Karolinska Institute. TB REACH is
   supported by Global Affairs Canada through grant number CA-3-D000920001.
   https://w05.inter
   national.gc.ca/projectbrowser-banqueprojets/projectprojet/details/d00092
   0001. Funders were not involved in the design of the study or
   collection, analysis, and interpretation of data or in writing the
   manuscript.},
Number-of-Cited-References = {30},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Hum. Resour. Health},
Doc-Delivery-Number = {ZR7AM},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000767931100002},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000743137100003,
Author = {Stilp, Adrienne M. and Emery, Leslie S. and Broome, Jai G. and Buth,
   Erin J. and Khan, Alyna T. and Laurie, Cecelia A. and Wang, Fei Fei and
   Wong, Quenna and Chen, Dongquan and D'Augustine, Catherine M. and
   Heard-Costa, Nancy L. and Hohensee, Chancellor R. and Johnson, William
   Craig and Juarez, Lucia D. and Liu, Jingmin and Mutalik, Karen M. and
   Raffield, Laura M. and Wiggins, Kerri L. and de Vries, Paul S. and
   Kelly, Tanika N. and Kooperberg, Charles and Natarajan, Pradeep and
   Peloso, Gina M. and Peyser, Patricia A. and Reiner, Alex P. and Arnett,
   Donna K. and Aslibekyan, Stella and Barnes, Kathleen C. and Bielak,
   Lawrence F. and Bis, Joshua C. and Cade, Brian E. and Chen, Ming-Huei
   and Correa, Adolfo and Cupples, L. Adrienne and de Andrade, Mariza and
   Ellinor, Patrick T. and Fornage, Myriam and Franceschini, Nora and Gan,
   Weiniu and Ganesh, Santhi K. and Graffelman, Jan and Grove, Megan L. and
   Guo, Xiuqing and Hawley, Nicola L. and Hsu, Wan-Ling and Jackson,
   Rebecca D. and Jaquish, Cashell E. and Johnson, Andrew D. and Kardia,
   Sharon L. R. and Kelly, Shannon and Lee, Jiwon and Mathias, Rasika A.
   and McGarvey, Stephen T. and Mitchell, Braxton D. and Montasser, May E.
   and Morrison, Alanna C. and North, Kari E. and Nouraie, Seyed Mehdi and
   Oelsner, Elizabeth C. and Pankratz, Nathan and Rich, Stephen S. and
   Rotter, I, Jerome and Smith, Jennifer A. and Taylor, Kent D. and Vasan,
   Ramachandran S. and Weeks, Daniel E. and Weiss, Scott T. and Wilson,
   Carla G. and Yanek, Lisa R. and Psaty, Bruce M. and Heckbert, Susan R.
   and Laurie, Cathy C.},
Title = {A System for Phenotype Harmonization in the National Heart, Lung, and
   Blood Institute Trans-Omics for Precision Medicine (TOPMed) Program},
Journal = {AMERICAN JOURNAL OF EPIDEMIOLOGY},
Year = {2021},
Volume = {190},
Number = {10},
Pages = {1977-1992},
Month = {OCT},
Abstract = {Genotype-phenotype association studies often combine phenotype data from
   multiple studies to increase statistical power. Harmonization of the
   data usually requires substantial effort due to heterogeneity in
   phenotype definitions, study design, data collection procedures, and
   data-set organization. Here we describe a centralized system for
   phenotype harmonization that includes input from phenotype domain and
   study experts, quality control, documentation, reproducible results, and
   data-sharing mechanisms. This system was developed for the National
   Heart, Lung, and Blood Institute's Trans-Omics for Precision Medicine
   (TOPMed) program, which is generating genomic and other-omics data for
   more than 80 studies with extensive phenotype data. To date, 63
   phenotypes have been harmonized across thousands of participants
   (recruited in 1948-2012) from up to 17 studies per phenotype. Here we
   discuss challenges in this undertaking and how they were addressed. The
   harmonized phenotype data and associated documentation have been
   submitted to National Institutes of Health data repositories for
   controlled access by the scientific community. We also provide materials
   to facilitate future harmonization efforts by the community, which
   include 1) the software code used to generate the 63 harmonized
   phenotypes, enabling others to reproduce, modify, or extend these
   harmonizations to additional studies, and 2) the results of labeling
   thousands of phenotype variables with controlled vocabulary terms.},
Publisher = {OXFORD UNIV PRESS INC},
Address = {JOURNALS DEPT, 2001 EVANS RD, CARY, NC 27513 USA},
Type = {Article},
Language = {English},
Affiliation = {Stilp, AM (Corresponding Author), Univ Washington, Sch Publ Hlth, Dept Biostat, Box 359461, Seattle, WA 98195 USA.
   Stilp, Adrienne M.; Emery, Leslie S.; Broome, Jai G.; Buth, Erin J.; Khan, Alyna T.; Laurie, Cecelia A.; Wang, Fei Fei; Wong, Quenna; Johnson, William Craig; Graffelman, Jan; Hsu, Wan-Ling; Laurie, Cathy C., Univ Washington, Sch Publ Hlth, Dept Biostat, Box 359461, Seattle, WA 98195 USA.
   Chen, Dongquan, Univ Alabama Birmingham, Sch Med, Dept Med, Birmingham, AL USA.
   Vasan, Ramachandran S., Boston Univ, Sch Med, Dept Med, Boston, MA 02118 USA.
   Heard-Costa, Nancy L., Boston Univ, Sch Med, Dept Neurol, Boston, MA 02118 USA.
   Hohensee, Chancellor R.; Liu, Jingmin; Kooperberg, Charles, Fred Hutchinson Canc Res Ctr, Div Publ Hlth Sci, 1124 Columbia St, Seattle, WA 98104 USA.
   Juarez, Lucia D., Univ Alabama Birmingham, Sch Med, Div Prevent Med, Birmingham, AL USA.
   Raffield, Laura M., Univ N Carolina, Dept Genet, Sch Med, Chapel Hill, NC 27515 USA.
   Wiggins, Kerri L.; Bis, Joshua C.; Psaty, Bruce M., Univ Washington, Sch Med, Dept Med, Cardiovasc Hlth Res Unit, Seattle, WA 98195 USA.
   de Vries, Paul S.; Fornage, Myriam; Morrison, Alanna C., Univ Texas Hlth Sci Ctr Houston, Human Genet Ctr, Sch Publ Hlth, Dept Epidemiol, Houston, TX 77030 USA.
   Kelly, Tanika N., Tulane Univ, Sch Publ Hlth \& Trop Med, Dept Epidemiol, New Orleans, LA USA.
   Natarajan, Pradeep, Massachusetts Gen Hosp, Cardiovasc Res Ctr, Boston, MA 02114 USA.
   Natarajan, Pradeep, Massachusetts Gen Hosp, Ctr Genom Med, Boston, MA 02114 USA.
   Natarajan, Pradeep; Weiss, Scott T., Harvard Univ, Harvard Med Sch, Dept Med, Boston, MA 02115 USA.
   Natarajan, Pradeep, Broad Inst MIT \& Harvard, Program Med \& Populat Genet, Cambridge, MA 02142 USA.
   Peloso, Gina M.; Cupples, L. Adrienne, Boston Univ, Sch Publ Hlth, Dept Biostat, Boston, MA USA.
   Peyser, Patricia A.; Bielak, Lawrence F.; Kardia, Sharon L. R.; Smith, Jennifer A., Univ Michigan, Sch Publ Hlth, Dept Epidemiol, Ann Arbor, MI 48109 USA.
   Reiner, Alex P.; Psaty, Bruce M.; Heckbert, Susan R., Univ Washington, Sch Publ Hlth, Dept Epidemiol, Seattle, WA 98195 USA.
   Reiner, Alex P., Fred Hutchinson Canc Res Ctr, 1124 Columbia St, Seattle, WA 98104 USA.
   Arnett, Donna K., Univ Kentucky, Deans Off, Lexington, KY USA.
   Aslibekyan, Stella, Univ Alabama Birmingham, Sch Publ Hlth, Dept Epidemiol, Birmingham, AL 35294 USA.
   Barnes, Kathleen C., Univ Colorado, Colorado Ctr Personalized Med, Sch Med, Aurora, CO USA.
   Cade, Brian E.; Lee, Jiwon, Brigham \& Womens Hosp, Dept Med, Div Sleep \& Circadian Disorders, 75 Francis St, Boston, MA 02115 USA.
   Cade, Brian E., Harvard Univ, Harvard Med Sch, Div Sleep Med, Boston, MA 02115 USA.
   Jaquish, Cashell E., NHLBI, Epidemiol Branch, Div Cardiovasc Sci, NIH, Bldg 10, Bethesda, MD 20892 USA.
   D'Augustine, Catherine M.; Heard-Costa, Nancy L.; Mutalik, Karen M.; Chen, Ming-Huei; Cupples, L. Adrienne; Johnson, Andrew D.; Vasan, Ramachandran S., Framingham Heart Dis Epidemiol Study, Framingham, MA USA.
   Chen, Ming-Huei; Johnson, Andrew D., NHLBI, Populat Sci Branch, Div Intramural Res, NIH, Bldg 10, Bethesda, MD 20892 USA.
   Correa, Adolfo, Univ Mississippi, Med Ctr, Dept Med, Jackson, MS 39216 USA.
   Correa, Adolfo, Univ Mississippi, Med Ctr, Dept Pediat, Jackson, MS 39216 USA.
   Correa, Adolfo, Univ Mississippi, John D Bower Sch Populat Hlth, Dept Populat Hlth Sci, Med Ctr, Jackson, MS 39216 USA.
   de Andrade, Mariza, Mayo Clin, Div Biomed Stat \& Informat, Rochester, MN USA.
   Ellinor, Patrick T., Broad Inst MIT \& Harvard, Cardiovasc Dis Initiat, Cambridge, MA 02142 USA.
   Fornage, Myriam, Univ Texas Hlth Sci Ctr Houston, Brown Fdn Inst Mol Med, McGovern Med Sch, Houston, TX 77030 USA.
   Franceschini, Nora; North, Kari E., Univ N Carolina, Dept Epidemiol, Gillings Sch Global Publ Hlth, Chapel Hill, NC 27515 USA.
   Gan, Weiniu, NHLBI, Airway Biol \& Dis Branch, Div Lung Dis, NIH, Bldg 10, Bethesda, MD 20892 USA.
   Ganesh, Santhi K., Univ Michigan, Dept Internal Med, Div Cardiovasc Med, Michigan Med, Ann Arbor, MI 48109 USA.
   Ganesh, Santhi K., Univ Michigan, Dept Human Genet, Michigan Med, Ann Arbor, MI 48109 USA.
   Graffelman, Jan, Tech Univ Catalonia, Dept Stat \& Operat Res, Barcelona, Spain.
   Grove, Megan L., Univ Texas Hlth Sci Ctr Houston, Sch Publ Hlth, Dept Epidemiol Human Genet \& Environm Sci, Houston, TX 77030 USA.
   Guo, Xiuqing; Rotter, Jerome, I; Taylor, Kent D., Harbor UCLA Med Ctr, Dept Pediat, Los Angeles Biomed Res Inst, Torrance, CA 90509 USA.
   Guo, Xiuqing; Rotter, Jerome, I; Taylor, Kent D., Harbor UCLA Med Ctr, Inst Translat Genom \& Populat Sci, Dept Pediat, Lundquist Inst Biomed Innovat, Torrance, CA 90509 USA.
   Hawley, Nicola L., Yale Univ, Yale Sch Publ Hlth, Dept Chron Dis Epidemiol, New Haven, CT USA.
   Jackson, Rebecca D., Ohio State Univ, Dept Internal Med, Div Endocrinol Diabet \& Metab, Columbus, OH 43210 USA.
   Kelly, Shannon, Vitalant Res Inst, Dept Epidemiol, San Francisco, CA USA.
   Kelly, Shannon, UCSF Benioff Childrens Hosp Oakland, Oakland, CA USA.
   Mathias, Rasika A.; Yanek, Lisa R., Johns Hopkins Univ, GeneSTAR Res Ctr, Sch Med, Div Gen Internal Med, Baltimore, MD USA.
   McGarvey, Stephen T., Brown Univ, Sch Publ Hlth, Int Hlth Inst, Providence, RI 02912 USA.
   McGarvey, Stephen T., Brown Univ, Sch Publ Hlth, Dept Epidemiol, Providence, RI 02912 USA.
   Mitchell, Braxton D.; Montasser, May E., Univ Maryland, Sch Med, Dept Med, Div Endocrinol Diabet \& Nutr, Baltimore, MD 21201 USA.
   Mitchell, Braxton D.; Montasser, May E., Univ Maryland, Sch Med, Dept Med, Program Personalized \& Genom Med, Baltimore, MD 21201 USA.
   Mitchell, Braxton D., Baltimore VA Med Ctr, Geriatr Res \& Educ Clin Ctr, Baltimore, MD USA.
   Nouraie, Seyed Mehdi, Univ Pittsburgh, Sch Med, Dept Med, Pittsburgh, PA 15213 USA.
   Oelsner, Elizabeth C., Columbia Univ, Dept Med, Vagelos Coll Phys \& Surg, New York, NY USA.
   Pankratz, Nathan, Univ Minnesota, Sch Med, Dept Lab Med \& Pathol, Minneapolis, MN 55455 USA.
   Rich, Stephen S., Univ Virginia, Sch Med, Ctr Publ Hlth Genom, Charlottesville, VA 22908 USA.
   Rich, Stephen S., Univ Virginia, Sch Med, Dept Publ Hlth Sci, Charlottesville, VA 22908 USA.
   Smith, Jennifer A., Univ Michigan, Survey Res Ctr, Inst Social Res, Ann Arbor, MI 48109 USA.
   Vasan, Ramachandran S., Boston Univ, Sch Publ Hlth, Dept Epidemiol, Boston, MA USA.
   Weeks, Daniel E., Univ Pittsburgh, Grad Sch Publ Hlth, Dept Human Genet, Pittsburgh, PA 15261 USA.
   Weeks, Daniel E., Univ Pittsburgh, Grad Sch Publ Hlth, Dept Biostat, Pittsburgh, PA 15261 USA.
   Weiss, Scott T., Brigham \& Womens Hosp, Dept Med, Channing Div Network Med, 75 Francis St, Boston, MA 02115 USA.
   Wilson, Carla G., Natl Jewish Hlth, Res Informat Serv, Denver, CO USA.
   Psaty, Bruce M., Univ Washington, Sch Publ Hlth, Dept Hlth Serv, Seattle, WA 98195 USA.
   Psaty, Bruce M.; Heckbert, Susan R., Kaiser Permanente Washington Hlth Res Inst, Seattle, WA USA.},
DOI = {10.1093/aje/kwab115},
ISSN = {0002-9262},
EISSN = {1476-6256},
Keywords = {cardiovascular disease; common data elements; hematologic disease;
   information dissemination; lung diseases; phenotypes; sleep-wake
   disorders},
Research-Areas = {Public, Environmental \& Occupational Health},
Web-of-Science-Categories  = {Public, Environmental \& Occupational Health},
Author-Email = {amstilp@uw.edu},
Affiliations = {University of Washington; University of Washington Seattle; University
   of Alabama System; University of Alabama Birmingham; Boston University;
   Boston University; Fred Hutchinson Cancer Center; University of Alabama
   System; University of Alabama Birmingham; University of North Carolina;
   University of North Carolina Chapel Hill; University of North Carolina
   School of Medicine; University of Washington; University of Washington
   Seattle; University of Texas System; University of Texas Health Science
   Center Houston; University of Texas School Public Health; Tulane
   University; Harvard University; Massachusetts General Hospital; Harvard
   University; Massachusetts General Hospital; Harvard University; Harvard
   Medical School; Harvard University; Massachusetts Institute of
   Technology (MIT); Broad Institute; Boston University; University of
   Michigan System; University of Michigan; University of Washington;
   University of Washington Seattle; Fred Hutchinson Cancer Center;
   University of Kentucky; University of Alabama System; University of
   Alabama Birmingham; University of Colorado System; University of
   Colorado Anschutz Medical Campus; Harvard University; Brigham \& Women's
   Hospital; Harvard University; Harvard Medical School; National
   Institutes of Health (NIH) - USA; NIH National Heart Lung \& Blood
   Institute (NHLBI); Framingham Heart Study; National Institutes of Health
   (NIH) - USA; NIH National Heart Lung \& Blood Institute (NHLBI);
   University of Mississippi Medical Center; University of Mississippi;
   University of Mississippi Medical Center; University of Mississippi;
   University of Mississippi Medical Center; University of Mississippi;
   Mayo Clinic; Harvard University; Massachusetts Institute of Technology
   (MIT); Broad Institute; University of Texas System; University of Texas
   Health Science Center Houston; University of North Carolina; University
   of North Carolina Chapel Hill; National Institutes of Health (NIH) -
   USA; NIH National Heart Lung \& Blood Institute (NHLBI); University of
   Michigan System; University of Michigan; University of Michigan System;
   University of Michigan; Universitat Politecnica de Catalunya; University
   of Texas System; University of Texas Health Science Center Houston;
   University of Texas School Public Health; Lundquist Institute;
   University of California System; University of California Los Angeles;
   University of California Los Angeles Medical Center; University of
   California System; University of California Los Angeles; University of
   California Los Angeles Medical Center; Yale University; University
   System of Ohio; Ohio State University; Vitalant; Vitalant Research
   Institute; University of California System; University of California San
   Francisco; UCSF Medical Center; UCSF Benioff Children's Hospital
   Oakland; Johns Hopkins University; Brown University; Brown University;
   University System of Maryland; University of Maryland Baltimore;
   University System of Maryland; University of Maryland Baltimore;
   Geriatric Research Education \& Clinical Center; US Department of
   Veterans Affairs; Veterans Health Administration (VHA); Baltimore VA
   Medical Center; Pennsylvania Commonwealth System of Higher Education
   (PCSHE); University of Pittsburgh; Columbia University; University of
   Minnesota System; University of Minnesota Twin Cities; University of
   Virginia; University of Virginia; University of Michigan System;
   University of Michigan; Boston University; Pennsylvania Commonwealth
   System of Higher Education (PCSHE); University of Pittsburgh;
   Pennsylvania Commonwealth System of Higher Education (PCSHE); University
   of Pittsburgh; Harvard University; Brigham \& Women's Hospital; National
   Jewish Health; University of Washington; University of Washington
   Seattle; Kaiser Permanente},
ResearcherID-Numbers = {Nouraie, Seyed Mehdi/GPW-8812-2022
   Ripke, Stephan/AAK-5486-2021
   Nouraie, Seyed Mehdi/O-4071-2018
   Graffelman, Jan/L-8056-2014
   Rotter, Jerome/AAY-6598-2021
   Natarajan, Pradeep/H-9764-2019
   Mathias, Rasika A/IAM-5259-2023
   Mitchell, Braxton/CAF-0876-2022
   Cade, Brian/J-6770-2019
   },
ORCID-Numbers = {Nouraie, Seyed Mehdi/0000-0001-7465-0581
   Graffelman, Jan/0000-0003-3900-0780
   Natarajan, Pradeep/0000-0001-8402-7435
   Mathias, Rasika A/0000-0002-2282-9042
   Weeks, Daniel/0000-0001-9410-7228
   Rich, Stephen/0000-0003-3872-7793
   Smith, Jennifer Ann/0000-0002-3575-5468
   Franceschini, Nora/0009-0001-8346-3662
   Cade, Brian/0000-0003-1424-0673
   Lee, Jiwon/0000-0002-4079-7494
   Raffield, Laura/0000-0002-7892-193X
   Kelly, Tanika/0000-0002-7348-4451},
Funding-Acknowledgement = {National Heart, Lung, and Blood Institute (NHLBI), NIH; TOPMed Data
   Coordinating Center {[}R01HL-120393, U01HL-120393, HHSN268201800001I,
   3R01HL-120393-02S1]; NHLBI {[}HHSN26820180001I, 5 U01 HL 120393-04, 3
   U01 HL 120393-04S2, HHSN268201700001I, HHSN268201700002I,
   HHSN268201700003I, HHSN268201700004I, HHSN268201700005I,
   HHSN268201800005I, HHSN268201800007I, AG0005, HHSN268201200036C,
   HHSN268200800007C, HHSN268201800001C, N01HC55222]; NIH Office of the
   Director , NIH Data Commons Pilot Phase Consortium; American Heart
   Association {[}18CDA34110116]; NHLBI Pooled Cohorts Study; Evans Medical
   Foundation; Department of Medicine, Boston University School of
   Medicine; Northwestern University {[}HHSN268201800003I]; University of
   Minnesota {[}HHSN268201800006I]; Kaiser Foundation Research Institute
   {[}HHSN268201800004I]; National Institute on Aging {[}AG0005,
   R01AG023629]; National Institute of Neurological Disorders and Stroke;
   COPD Foundation; University of North Carolina
   {[}HHSN268201300001I/N01-HC-65233]; University of Miami
   {[}HHSN268201300004I/N01-HC-65234]; Albert Einstein College of Medicine
   {[}HHSN268201300002I/N01-HC-65235]; University of Illinois at Chicago
   {[}HHSN268201300003I/N01HC-65236]; San Diego State University
   {[}HHSN268201300005I/N01HC-65237]; Jackson State University through
   NHLBI {[}HHSN268201800013I]; Tougaloo College through NHLBI
   {[}HHSN268201800014I]; Mississippi State Department of Health through
   NHLBI {[}HHSN268201800015I]; University of Mississippi Medical Center
   through NHLBI {[}HHSN268201800010I, HHSN268201800011I,
   HHSN268201800012I]; National Institute on Minority Health and Health
   Disparities; National Human Genome Research Institute {[}HG04735,
   HG06379]; Mayo Foundation; Broad Institute of MIT and Harvard
   (Cambridge, Massachusetts) {[}3U54HG003067-13S1]; TOPMed Informatics
   Research Center {[}3R01HL-117626-02S1]; Samoan Ministry of Health; Samoa
   Bureau of Statistics; Seven Bridges Genomics Inc. (Charlestown,
   Massachusetts); Johnson \& Johnson (New Brunswick, New Jersey); AMGen,
   Inc. (Thousand Oaks, California); National Institutes of Health (NIH),
   US Department of Health and Human Services; NIH {[}R01-MD012765,
   R01-DK117445, R21-HL140385, R01HL092577, R01HL128914, K24HL105780,
   R01HL130733, R21-HL129924, K23-HL130627, R01HL122684]; University of
   Alabama at Birmingham {[}HHSN268201800005I, HHSN268201800007I]; National
   Institute on Deafness and Other Communication Disorders; National
   Institute of Dental and Craniofacial Research; National Institute of
   Diabetes and Digestive and Kidney Diseases; NIH Office of Dietary
   Supplements; the NHLBI {[}HHSN268201300001I/N01-HC-65233,
   75N92019D00031, HL054457, HL054464, HL054481, HL119443, HL087660,
   HL085571, U01 HL072524, R01 HL104135, R01 HL104135-04S1, HL068986,
   HL085251]; `the NHLBI' {[}N01HC85079, N01HC85080, N01HC85081,
   N01HC85082, N01HC85083, N01HC85086, U01HL080295, U01HL130114, U01
   HL089897, U01 HL089856, R37 HL066289-14, P01 HL132825, NO1-HC-25195,
   HHSN268201500001I]; the NIH {[}N01-HC-95159, 75N92020D00005,
   N01-HC-95160, 75N92020D00002, N01-HC-95161, 75N92020D00003,
   N01-HC-95162, 75N92020D00006, N01-HC-95163, 75N92020D00004,
   N01-HC-95164, 75N92020D00007, N01-HC-95165, N01-HC-95166, N01-HC-95167,
   N01-HC-95168, N01-HC-95169, UL1-TR-000040, UL1-TR-001079, UL1-TR-001420,
   UL1-TR-001881, DK063491]; `the NIH' {[}R01HL139672, K01-HL135405,
   R01HL142711, R01 HL121007, U01 HL072515, R01 AG18728, R01-HL046380,
   KL2-RR024990, R35-HL135818, R01-HL113338, 75N92020D00001,
   HHSN268201500003I]; ``the NHLBI{''} {[}HL095080, HL073410, HL66216,
   HL83141, N02-HL-64278, HHSN268201600018C, HHSN268201600001C,
   HHSN268201600002C, HHSN268201600003C, HHSN268201600004C];  {[}R01
   HL092577-06S1]},
Funding-Text = {This work was funded by numerous grants and contracts from the National
   Institutes of Health (NIH), US Department of Health and Human Services.
   The Trans-Omics in Precision Medicine (TOPMed) program was supported by
   the National Heart, Lung, and Blood Institute (NHLBI), NIH, with core
   services provided by the TOPMed Informatics Research Center (award
   3R01HL-117626-02S1; contract HHSN268201800002I) and the TOPMed Data
   Coordinating Center (awards R01HL-120393 and U01HL-120393; contract
   HHSN268201800001I). Whole-genome sequencing for TOPMed was supported by
   the NHLBI. Phenotype harmonization activities were funded in part by the
   NHLBI (contract HHSN26820180001I).; Additional harmonization funding was
   provided by the NHLBI (grant 5 U01 HL 120393-04). Phenotype variable
   tagging was funded by the NHLBI (grant supplement 3 U01 HL 120393-04S2)
   and the NIH Office of the Director as part of the NIH Data Commons Pilot
   Phase Consortium. Additional financial support was provided to some
   authors: N.F. was additionally supported by NIH grants R01-MD012765,
   R01-DK117445, and R21-HL140385. P.T.E. was additionally supported by NIH
   grants R01HL092577, R01HL128914, and K24HL105780. A.P.R. was
   additionally supported by NIH grant R01HL130733. P.S.d.V. was
   additionally supported by American Heart Association grant
   18CDA34110116. E.C.O. was additionally supported by the NHLBI Pooled
   Cohorts Study and NIH grants R21-HL129924 and K23-HL130627. S.K.G. was
   additionally supported by NIH grants R01HL122684 and R01HL139672. B.E.C.
   was additionally supported by NIH grant K01-HL135405. P.N. and G.M.P.
   were additionally supported by NIH grant R01HL142711. R.S.V. was
   supported in part by the Evans Medical Foundation and the Jay and Louis
   Coffman Endowment from the Department of Medicine, Boston University
   School of Medicine.; Financial support for individual TOPMed studies was
   provided by the following-Genetics of Cardiometabolic Health in the
   Amish: The TOPMed component of the Amish Research Program was supported
   by NIH grants R01 HL121007, U01 HL072515, and R01 AG18728.
   Atherosclerosis Risk in Communities (ARIC) Study: The ARIC Study has
   been funded in whole or in part by the NHLBI (contracts
   HHSN268201700001I, HHSN268201700002I, HHSN268201700003I,
   HHSN268201700004I, and HHSN268201700005I). Coronary Artery Risk
   Development in Young Adults (CARDIA) Study: The CARDIA Study is
   conducted and supported by the NHLBI in collaboration with the
   University of Alabama at Birmingham (awards HHSN268201800005I and
   HHSN268201800007I), Northwestern University (award HHSN268201800003I),
   the University of Minnesota (award HHSN268201800006I), and the Kaiser
   Foundation Research Institute (award HHSN268201800004I). CARDIA is also
   partially supported by the Intramural Research Program of the National
   Institute on Aging and an Intra-Agency Agreement (agreement AG0005)
   between the National Institute on Aging and the NHLBI. Cleveland Family
   Study: The Cleveland Family Study has been supported in part by the NIH
   (grants R01-HL046380, KL2-RR024990, R35-HL135818, and R01-HL113338).
   Cardiovascular Health Study (CHS): The CHS was supported by contracts
   HHSN268201200036C, HHSN268200800007C, HHSN268201800001C, N01HC55222,
   N01HC85079, N01HC85080, N01HC85081, N01HC85082, N01HC85083, and
   N01HC85086 and grants U01HL080295 and U01HL130114 from the NHLBI, with
   additional contributions from the National Institute of Neurological
   Disorders and Stroke. Additional support was provided by the National
   Institute on Aging (award R01AG023629). Genetic Epidemiology of COPD
   Study (COPDGene): The COPDGene project was supported by awards U01
   HL089897 and U01 HL089856 from the NHLBI. The COPDGene project is also
   supported by the COPD Foundation through contributions made to an
   industry advisory board comprised of AstraZeneca AB (Cambridge, United
   Kingdom), Boehringer Ingelheim (Ingelheim am Rhein, Germany),
   GlaxoSmithKline plc (London, United Kingdom), Novartis International AG
   (Basel, Switzerland), Pfizer, Inc. (New York, New York), Siemens
   Healthcare GmbH (Erlangen, Germany), and Sunovion Pharmaceuticals Inc.
   (Marlborough, Massachusetts). Genetic Epidemiology of Asthma in Costa
   Rica (CRA) Study: The CRA Study was funded by the NHLBI (grants R37
   HL066289-14 and P01 HL132825). Framingham Heart Study: The Framingham
   Heart Study was supported by contracts NO1-HC-25195, HHSN268201500001I,
   and 75N92019D00031 from the NHLBI and by grant supplement R01
   HL092577-06S1 for this research. Genetic Epidemiology Network of
   Arteriopathy (GENOA): Support for GENOA was provided by the NHLBI
   (awards HL054457, HL054464, HL054481, HL119443, HL087660, and HL085571).
   Genetics of Lipid Lowering Drugs and Diet Network (GOLDN): GOLDN
   biospecimens, baseline phenotype data, and intervention phenotype data
   were collected with funding from the NHLBI (grant U01 HL072524).
   Whole-genome sequencing in GOLDN was funded by the NHLBI (grant R01
   HL104135 and grant supplement R01 HL104135-04S1).; Hispanic Community
   Health Study/Study of Latinos (HCHS/SOL): The HCHS/SOL is a
   collaborative study supported by contracts between the NHLBI and the
   University of North Carolina (contract HHSN268201300001I/N01-HC-65233),
   the University of Miami (contract HHSN268201300004I/N01-HC-65234), the
   Albert Einstein College of Medicine (contract
   HHSN268201300002I/N01-HC-65235), and the University of Illinois at
   Chicago (contract HHSN268201300003I/N01HC-65236 Northwestern
   University), and San Diego State University (contract
   HHSN268201300005I/N01HC-65237). The following institutions have
   contributed to the HCHS/SOL through a transfer of funds to the NHLBI:
   the National Institute on Minority Health and Health Disparities, the
   National Institute on Deafness and Other Communication Disorders, the
   National Institute of Dental and Craniofacial Research, the National
   Institute of Diabetes and Digestive and Kidney Diseases, the National
   Institute of Neurological Disorders and Stroke, and the NIH Office of
   Dietary Supplements. Heart and Vascular Health Study: The Heart and
   Vascular Health Study was supported by the NHLBI (grants HL068986,
   HL085251,HL095080, and HL073410). Jackson Heart Study: The Jackson Heart
   Study is supported by and conducted in collaboration with Jackson State
   University (contract HHSN268201800013I), Tougaloo College (contract
   HHSN268201800014I), the Mississippi State Department of Health (contract
   HHSN268201800015I), and the University of Mississippi Medical Center
   (contracts HHSN268201800010I, HHSN268201800011I, and HHSN268201800012I)
   through contracts from the NHLBI and the National Institute on Minority
   Health and Health Disparities. Mayo Clinic Venous Thromboembolism Study:
   The Mayo Clinic Venous Thromboembolism Study was funded, in part, by the
   NHLBI (grants HL66216 and HL83141), the National Human Genome Research
   Institute (grants HG04735 and HG06379), and the Mayo Foundation.
   Multi-Ethnic Study of Atherosclerosis (MESA): Whole-genome sequencing
   for MESA (dbGaP accession number phs001416.v1.p1) was performed at the
   Broad Institute of MIT and Harvard (Cambridge, Massachusetts) (award
   3U54HG003067-13S1). Centralized read mapping and genotype calling, along
   with variant quality metrics and filtering, were provided by the TOPMed
   Informatics Research Center (award 3R01HL-117626-02S1). Phenotype
   harmonization, data management, sample-identity quality control, and
   general study coordination were provided by the TOPMed Data Coordinating
   Center (award 3R01HL-120393-02S1). MESA and the MESA SHARe project are
   conducted and supported by the NHLBI in collaboration with the MESA
   investigators. Support for MESA is provided by NIH contracts
   75N92020D00001 (NHLBI), HHSN268201500003I (NHLBI), N01-HC-95159 (NHLBI),
   75N92020D00005 (NHLBI), N01-HC-95160 (NHLBI), 75N92020D00002 (NHLBI),
   N01-HC-95161 (NHLBI), 75N92020D00003 (NHLBI), N01-HC-95162 (NHLBI),
   75N92020D00006 (NHLBI), N01-HC-95163 (NHLBI), 75N92020D00004 (NHLBI),
   N01-HC-95164 (NHLBI), 75N92020D00007 (NHLBI), N01-HC-95165 (NHLBI),
   N01-HC-95166 (NHLBI), N01-HC-95167 (NHLBI), N01-HC-95168 (NHLBI),
   N01-HC-95169 (NHLBI), UL1-TR-000040 (National Center for Advancing
   Translational Sciences (NCATS) (Clinical and Translational Science
   Institute (CTSI))), UL1-TR-001079 (NCATS (CTSI)), UL1-TR-001420 (NCATS
   (CTSI)), UL1-TR-001881 (NCATS (CTSI)), and DK063491 (National Institute
   of Diabetes and Digestive and Kidney Diseases). Funding for SHARe
   genotyping was provided by NHLBI contract N02-HL-64278. Genotyping was
   performed at Affymetrix, Inc.; (Santa Clara, California) and the Broad
   Institute of MIT and Harvard using the Affymetrix Genome-Wide Human SNP
   Array 6.0. Samoan Adiposity Study: Data collection for the Samoan
   Adiposity Study was funded by NIH grant R01-HL093093. Women's Health
   Initiative: The Women's Health Initiative program is funded by the NHLBI
   (contracts HHSN268201600018C, HHSN268201600001C, HHSN268201600002C,
   HHSN268201600003C, and HHSN268201600004C).; The harmonized data
   presented in this paper have been submitted to the database of Genotypes
   and Phenotypes (dbGaP) and the NHLBI BioData Catalyst. The software code
   with which to reproduce the harmonized phenotypes presented in this
   paper from dbGaP files is available on GitHub (14). See the ``Data
   Availability{''} section of the text for details.; We gratefully
   acknowledge the researchers and study participants who provided
   biological samples and data for TOPMed. We acknowledge Drs. Mike Feolo
   and Masato Kimura for making the harmonized phenotype data and the
   phenotype tagging data available in dbGaP. We also acknowledge
   contributors to the overall TOPMed project, who can be found on the
   TOPMed Data Coordinating Center website
   (https://www.nhlbiwgs.org/topmed-bannerauthorship).The Genetics of
   Cardiometabolic Health in the Amish Study investigators gratefully thank
   the Amish community and research volunteers for their long-standing
   partnership, and they acknowledge the dedication of their Amish
   liaisons, fieldworkers, and the Amish Research Clinic staff, without
   whom these studies would not have been possible. The ARIC Study
   investigators thank the study staff and participants for their important
   contributions. The Framingham Heart Study investigators acknowledge the
   dedication of the study participants, without whom this research would
   not have been possible. The Jackson Heart Study investigators thank the
   study staff and participants. The Samoan Adiposity Study investigators
   thank the Samoan participants in the study and local village
   authorities.; They acknowledge the Samoan Ministry of Health and the
   Samoa Bureau of Statistics for their support of this research.; A.M.S.
   receives funding from Seven Bridges Genomics Inc. (Charlestown,
   Massachusetts) to develop tools for the NHLBI BioData Catalyst
   consortium. B.M.P. reports serving on the Steering Committee of the Yale
   Open Data Access Project, which is funded by Johnson \& Johnson (New
   Brunswick, New Jersey). S.A. reports being employed by and holding
   equity in 23andMe, Inc. (Sunnyvale, California). P.N. reports conflicts
   of interest unrelated to this work: grant support from AMGen, Inc.
   (Thousand Oaks, California), Apple Inc. (Cupertino, California), and
   Boston Scientific Corporation (Marlborough, Massachusetts) and
   consulting fees from Apple. M.E.M. receives funding from Regeneron
   Pharmaceuticals Inc. (Tarrytown, New York) unrelated to this work. The
   other authors have no potential conflicts of interest to declare.},
Number-of-Cited-References = {20},
Times-Cited = {18},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Am. J. Epidemiol.},
Doc-Delivery-Number = {YH4KH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000743137100003},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000794881100003,
Author = {Gad, Ahmed G. and Sallam, Karam M. and Chakrabortty, Ripon K. and Ryan,
   Michael J. and Abohany, Amr A.},
Title = {An improved binary sparrow search algorithm for feature selection in
   data classification},
Journal = {NEURAL COMPUTING \& APPLICATIONS},
Year = {2022},
Volume = {34},
Number = {18, SI},
Pages = {15705-15752},
Month = {SEP},
Abstract = {Feature Selection (FS) is an important preprocessing step that is
   involved in machine learning and data mining tasks for preparing data
   (especially high-dimensional data) by eliminating irrelevant and
   redundant features, thus reducing the potential curse of dimensionality
   of a given large dataset. Consequently, FS is arguably a combinatorial
   NP-hard problem in which the computational time increases exponentially
   with an increase in problem complexity. To tackle such a problem type,
   metaheuristic techniques have been opted by an increasing number of
   scholars. Herein, a novel meta-heuristic algorithm, called Sparrow
   Search Algorithm (SSA), is presented. The SSA still performs poorly on
   exploratory behavior and exploration-exploitation trade-off because it
   does not duly stimulate the search within feasible regions, and the
   exploitation process suffers noticeable stagnation. Therefore, we
   improve SSA by adopting: i) a strategy for Random Re-positioning of
   Roaming Agents (3RA); and ii) a novel Local Search Algorithm (LSA),
   which are algorithmically incorporated into the original SSA structure.
   To the FS problem, SSA is improved and cloned as a binary variant,
   namely, the improved Binary SSA (iBSSA), which would strive to select
   the optimal or near-optimal features from a given dataset while keeping
   the classification accuracy maximized For binary conversion, the iBSSA
   was primarily validated against nine common S-shaped and V-shaped
   Transfer Functions (TFs), thus producing nine iBSSA variants. To verify
   the robustness of these variants, three well-known classification
   techniques, including k-Nearest Neighbor (k-NN), Support Vector Machine
   (SVM), and Random Forest (RF) were adopted as fitness evaluators with
   the proposed iBSSA approach and many other competing algorithms, on 18
   multifaceted, multi-scale benchmark datasets from the University of
   California Irvine (UCI) data repository. Then, the overall
   best-performing iBSSA variant for each of the three classifiers was
   compared with binary variants of 12 different well-known meta-heuristic
   algorithms, including the original SSA (BSSA), Artificial Bee Colony
   (BABC), Particle Swarm Optimization (BPSO), Bat Algorithm (BBA), Grey
   Wolf Optimization (BGWO), Whale Optimization Algorithm (BWOA),
   Grasshopper Optimization Algorithm (BGOA) SailFish Optimizer (BSFO),
   Harris Hawks Optimization (BHHO), Bird Swarm Algorithm (BBSA), Atom
   Search Optimization (BASO), and Henry Gas Solubility Optimization
   (BHGSO). Based on a Wilcoxon's non-parametric statistical test (alpha =
   0.05), the superiority of iBSSA with the three classifiers was very
   evident against counterparts across the vast majority of the selected
   datasets, achieving a feature size reduction of up to 92\% along with up
   to 100\% classification accuracy on some of those datasets.},
Publisher = {SPRINGER LONDON LTD},
Address = {236 GRAYS INN RD, 6TH FLOOR, LONDON WC1X 8HL, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Gad, AG (Corresponding Author), Kafrelsheikh Univ, Fac Comp \& Informat, Kafrelsheikh, Egypt.
   Gad, Ahmed G.; Abohany, Amr A., Kafrelsheikh Univ, Fac Comp \& Informat, Kafrelsheikh, Egypt.
   Sallam, Karam M., Zagazig Univ, Fac Comp \& Informat, Zagazig, Egypt.
   Sallam, Karam M., Univ Canberra, Fac Sci \& Technol, Sch IT \& Syst, Canberra, ACT 2601, Australia.
   Chakrabortty, Ripon K., UNSW Canberra ADFA, Sch Engn \& IT, Capabil Syst Ctr, Canberra, ACT, Australia.
   Ryan, Michael J., Capabil Associates Canberra, Canberra, ACT, Australia.},
DOI = {10.1007/s00521-022-07203-7},
EarlyAccessDate = {APR 2022},
ISSN = {0941-0643},
EISSN = {1433-3058},
Keywords = {Machine learning; Classification; Feature selection; Meta-heuristics;
   Sparrow search algorithm; Combinatorial optimization; Swarm-based
   optimization; Pattern recognition; Data mining; Binary optimization},
Keywords-Plus = {WHALE OPTIMIZATION ALGORITHM; PARTICLE SWARM OPTIMIZATION; GENETIC
   ALGORITHM; EVOLUTIONARY; MODEL},
Research-Areas = {Computer Science},
Web-of-Science-Categories  = {Computer Science, Artificial Intelligence},
Author-Email = {ahmed.gad@fci.kfs.edu.eg
   karam\_sallam@zu.edu.eg
   r.chakrabortty@adfa.edu.au
   mike.ryan@ieee.org
   amrabohany8@gmail.com},
Affiliations = {Egyptian Knowledge Bank (EKB); Kafrelsheikh University; Egyptian
   Knowledge Bank (EKB); Zagazig University; University of Canberra;
   Australian Defense Force Academy},
ResearcherID-Numbers = {Chakrabortty, Ripon K/ABA-6480-2020
   Gad, Ahmed G./AAO-2077-2021
   sallam, karam/J-2387-2019
   },
ORCID-Numbers = {Chakrabortty, Ripon K/0000-0002-7373-0149
   Gad, Ahmed G./0000-0002-2671-041X
   sallam, karam/0000-0003-4039-1897
   Sallam, Karam/0000-0001-5767-2818},
Funding-Acknowledgement = {Science, Technology \& Innovation Funding Authority (STDF); Egyptian
   Knowledge Bank (EKB)},
Funding-Text = {Open access funding provided by The Science, Technology \& Innovation
   Funding Authority (STDF) in cooperation with The Egyptian Knowledge Bank
   (EKB).},
Number-of-Cited-References = {132},
Times-Cited = {18},
Usage-Count-Last-180-days = {7},
Usage-Count-Since-2013 = {40},
Journal-ISO = {Neural Comput. Appl.},
Doc-Delivery-Number = {3Z6BV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000794881100003},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000636421400005,
Author = {Weber, Simone and Kissinger, Thomas and Chehura, Edmond and Staines,
   Stephen and Barrington, James and Mullaney, Kevin and Fragonara, Luca
   Zanotti and Petrunin, Ivan and James, Stephen and Lone, Mudassir and
   Tatam, Ralph},
Title = {Application of fibre optic sensing systems to measure rotor blade
   structural dynamics},
Journal = {MECHANICAL SYSTEMS AND SIGNAL PROCESSING},
Year = {2021},
Volume = {158},
Month = {SEP},
Abstract = {This paper compares two fibre optic sensing techniques for vibration
   characterisation: (a) optical fibre Bragg grating (FBG) strain gauges
   and (b) a novel direct fibre optic shape sensing (DFOSS) approach based
   on differential interferometric strain measurements between multiple
   fibres within the same fibre arrangement. Operational mode shapes and
   frequency measurements of an Airbus Helicopters H135 bearingless main
   rotor blade (5.1 m radius) were acquired during a series of ground
   vibration tests undertaken in a controlled laboratory environment. Data
   recorded by the fibre optic instrumentation systems were validated using
   commercially available accelerometers and compared against a baseline
   finite element model. Both fibre optic sensing systems proved capable of
   identifying the natural frequencies of the blade in the frequency range
   of interest (0-100 Hz). The data from the FBG sensors exhibited a
   dependency on their position relative to the neutral axes of the blade,
   which meant that full characterisation of the flapping and lagging modes
   required careful consideration of sensor location in the chordwise
   direction. The DFOSS system was able to identify all structural
   dynamics, despite being located on the neutral axis in the lagging
   direction, due to its sensitivity to angle changes, rather than strain,
   and its biaxial measurement capability. The DFOSS system also allowed
   the operational mode shapes of the blade to be determined directly,
   without the requirement for strain transfer from the blade to the sensor
   and without the requirement for a model of the underlying structure. The
   accuracy of obtained natural frequencies and operational mode shapes is
   assessed, demonstrating the potential of the use of both fibre optic
   sensing systems for determining blade structural dynamics.
   (c) 2021 The Authors. Published by Elsevier Ltd. This is an open access
   article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD},
Address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Tatam, R (Corresponding Author), Cranfield Univ, Ctr Engn Photon, Cranfield MK43 0AL, Beds, England.
   Weber, Simone, Airbus Helicopters UK Ltd, 128 Langford Ln, Kidlington OX5 1QZ, England.
   Kissinger, Thomas; Chehura, Edmond; Staines, Stephen; Barrington, James; Mullaney, Kevin; James, Stephen; Tatam, Ralph, Cranfield Univ, Ctr Engn Photon, Cranfield MK43 0AL, Beds, England.
   Weber, Simone; Lone, Mudassir, Cranfield Univ, Ctr Aeronaut, Cranfield MK43 0AL, Beds, England.
   Fragonara, Luca Zanotti; Petrunin, Ivan, Cranfield Univ, Ctr Autonomous \& Cyberphys Syst, Cranfield MK43 0AL, Beds, England.},
DOI = {10.1016/j.ymssp.2021.107758},
EarlyAccessDate = {MAR 2021},
Article-Number = {107758},
ISSN = {0888-3270},
EISSN = {1096-1216},
Keywords = {Bearingless main rotor blade; Fibre Bragg gratings; Shape measurement},
Keywords-Plus = {OPTIMAL PLACEMENT; STRAIN; INTERFEROMETRY; SENSORS},
Research-Areas = {Engineering},
Web-of-Science-Categories  = {Engineering, Mechanical},
Author-Email = {r.p.tatam@cranfield.ac.uk},
Affiliations = {Cranfield University; Cranfield University; Cranfield University},
ResearcherID-Numbers = {Kissinger, Thomas/P-5540-2015
   Tatam, Ralph P/N-2222-2014
   James, Stephen Wayne/E-6212-2012
   Fragonara, Luca Zanotti/I-5832-2019
   },
ORCID-Numbers = {Kissinger, Thomas/0000-0003-1832-7143
   James, Stephen Wayne/0000-0003-0651-9842
   Fragonara, Luca Zanotti/0000-0001-6269-5280
   Barrington, James/0000-0002-1177-5616
   Petrunin, Ivan/0000-0002-8705-5308},
Funding-Acknowledgement = {Innovate UK via the Aerospace Technology Institute (ATI) {[}ATI 102381];
   Engineering and Physical Sciences Research Council (EPSRC) UK
   {[}EP/N002520/1]},
Funding-Text = {The authors would like to acknowledge funding from Innovate UK via the
   Aerospace Technology Institute (ATI) as part of the BladeSense project
   (ATI 102381) . We also acknowledge funding from the Engineering and
   Physical Sciences Research Council (EPSRC) UK via grant EP/N002520/1.
   The underlying data can be accessed from the Cranfield Online Research
   Data Repository at https://doi.org/10.17862/cranfield.rd.13806794.},
Number-of-Cited-References = {61},
Times-Cited = {10},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {43},
Journal-ISO = {Mech. Syst. Signal Proc.},
Doc-Delivery-Number = {RH7VN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000636421400005},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000503451800014,
Author = {Hitchcock, Caitlin and Newby, Jill and Timm, Emma and Howard, Rachel M.
   and Golden, Ann-Marie and Kuyken, Willem and Dalgleish, Tim},
Title = {Memory Category Fluency, Memory Specificity, and the Fading Affect Bias
   for Positive and Negative Autobiographical Events: Performance on a Good
   Day-Bad Day Task in Healthy and Depressed Individuals},
Journal = {JOURNAL OF EXPERIMENTAL PSYCHOLOGY-GENERAL},
Year = {2020},
Volume = {149},
Number = {1},
Pages = {198-206},
Month = {JAN},
Abstract = {In mentally healthy individuals, autobiographical memory is typically
   biased toward positive events, which may help to maintain psychological
   well-being. Our aim was to assess a range of important positive memory
   biases in the mentally healthy and explore the possibility that these
   biases are mitigated in those with mental health problems. We
   administered a novel recall paradigm that required recollection of
   multiple good and bad past events (the Good Day-Bad Day task) to healthy
   and depressed individuals. This allowed us to explore differences in
   memory category fluency (i.e., the ability to generate integrated sets
   of associated events) for positive and negative memories, along with
   memory specificity, and fading affect bias-a greater reduction in the
   intensity of memory-related affect over time for negative versus
   positive events. We found that healthy participants demonstrated
   superior category fluency for positive relative to negative events but
   that this effect was absent in depressed participants. Healthy
   participants exhibited a strong fading affect bias that was
   significantly mitigated, although still present, in depression. Finally,
   memory specificity was reduced in depression for both positive and
   negative memories. Findings demonstrate that the positive bias
   associated with mental health is maintained by multiple autobiographical
   memory processes and that depression is as much a function of the
   absence of these positive biases as it is the presence of negative
   biases. Results provide important guidance for developing new treatments
   for improving mental health.},
Publisher = {AMER PSYCHOLOGICAL ASSOC},
Address = {750 FIRST ST NE, WASHINGTON, DC 20002-4242 USA},
Type = {Article},
Language = {English},
Affiliation = {Dalgleish, T (Corresponding Author), Univ Cambridge, MRC Cognit \& Brain Sci Unit, 15 Chaucer Rd, Cambridge CB2 7EF, England.
   Hitchcock, Caitlin; Newby, Jill; Timm, Emma; Howard, Rachel M.; Golden, Ann-Marie; Dalgleish, Tim, Univ Cambridge, MRC Cognit \& Brain Sci Unit, 15 Chaucer Rd, Cambridge CB2 7EF, England.
   Kuyken, Willem, Univ Oxford, Dept Psychiat, Oxford, England.
   Dalgleish, Tim, Cambridgeshire \& Peterborough NHS Fdn Trust, Cambridge, England.},
DOI = {10.1037/xge0000617},
ISSN = {0096-3445},
EISSN = {1939-2222},
Keywords = {autobiographical memory; positive bias; mental health; depression},
Keywords-Plus = {SELF; ACCESSIBILITY; FUTURE; MOOD; PLEASANT; RECALL; STYLE; LIFE; AGE},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Experimental},
Author-Email = {tim.dalgleish@mrc-cbu.cam.ac.uk},
Affiliations = {University of Cambridge; University of Oxford},
ResearcherID-Numbers = {Kuyken, Willem/ABC-5152-2021
   },
ORCID-Numbers = {Kuyken, Willem/0000-0002-8596-5252
   Newby, Jill/0000-0002-6473-9811
   Hitchcock, Caitlin/0000-0002-2435-0713},
Funding-Acknowledgement = {United Kingdom Medical Research Council {[}SUAG/006/RG91365]; United
   Kingdom National Institute of Health Research Cambridge Biomedical
   Research Centre; ESRC {[}ES/R010781/1] Funding Source: UKRI; MRC
   {[}MC\_UU\_00005/4] Funding Source: UKRI},
Funding-Text = {This research was supported by the United Kingdom Medical Research
   Council (Grant: SUAG/006/RG91365) and the United Kingdom National
   Institute of Health Research Cambridge Biomedical Research Centre. A
   preprint of this article was made available through the Open Science
   Framework in April 2018 and can be viewed at https://osf.io/9w6zk/.Study
   data and scripts used in analysis are freely available through the MRC
   Cognition and Brain Sciences Unit's Open Data Repository, which can be
   accessed via www.mrc-cbu.cam.ac.uk/publications/opendata.},
Number-of-Cited-References = {50},
Times-Cited = {16},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {21},
Journal-ISO = {J. Exp. Psychol.-Gen.},
Doc-Delivery-Number = {JX0RQ},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000503451800014},
OA = {Green Published, hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000716459500001,
Author = {Dorigo, Wouter and Himmelbauer, Irene and Aberer, Daniel and Schremmer,
   Lukas and Petrakovic, Ivana and Zappa, Luca and Preimesberger, Wolfgang
   and Xaver, Angelika and Annor, Frank and Ardo, Jonas and Baldocchi,
   Dennis and Bitelli, Marco and Bloeschl, Gunter and Bogena, Heye and
   Brocca, Luca and Calvet, Jean-Christophe and Julio Camarero, J. and
   Capello, Giorgio and Choi, Minha and Cosh, Michael C. and van de Giesen,
   Nick and Hajdu, Istvan and Ikonen, Jaakko and Jensen, Karsten H. and
   Kanniah, Kasturi Devi and de Kat, Ileen and Kirchengast, Gottfried and
   Rai, Pankaj Kumar and Kyrouac, Jenni and Larson, Kristine and Liu, Suxia
   and Loew, Alexander and Moghaddam, Mahta and Martinez Fernandez, Jose
   and Mattar Bader, Cristian and Morbidelli, Renato and Musial, Jan P. and
   Osenga, Elise and Palecki, Michael A. and Pellarin, Thierry and
   Petropoulos, George P. and Pfeil, Isabella and Powers, Jarrett and
   Robock, Alan and Rudiger, Christoph and Rummel, Udo and Strobel, Michael
   and Su, Zhongbo and Sullivan, Ryan and Tagesson, Torbern and Varlagin,
   Andrej and Vreugdenhil, Mariette and Walker, Jeffrey and Wen, Jun and
   Wenger, Fred and Wigneron, Jean Pierre and Woods, Mel and Yang, Kun and
   Zeng, Yijian and Zhang, Xiang and Zreda, Marek and Dietrich, Stephan and
   Gruber, Alexander and van Oevelen, Peter and Wagner, Wolfgang and
   Scipal, Klaus and Drusch, Matthias and Sabia, Roberto},
Title = {The International Soil Moisture Network: serving Earth system science
   for over a decade},
Journal = {HYDROLOGY AND EARTH SYSTEM SCIENCES},
Year = {2021},
Volume = {25},
Number = {11},
Pages = {5749-5804},
Month = {NOV 9},
Abstract = {In 2009, the International Soil Moisture Network (ISMN) was initiated as
   a community effort, funded by the European Space Agency, to serve as a
   centralised data hosting facility for globally available in situ soil
   moisture measurements (Dorigo et al., 2011b, a). The ISMN brings
   together in situ soil moisture measurements collected and freely shared
   by a multitude of organisations, harmonises them in terms of units and
   sampling rates, applies advanced quality control, and stores them in a
   database. Users can freely retrieve the data from this database through
   an online web portal (https://ismn.earth/en/, last access: 28 October
   2021). Meanwhile, the ISMN has evolved into the primary in situ soil
   moisture reference database worldwide, as evidenced by more than 3000
   active users and over 1000 scientific publications referencing the data
   sets provided by the network. As of July 2021, the ISMN now contains the
   data of 71 networks and 2842 stations located all over the globe, with a
   time period spanning from 1952 to the present. The number of networks
   and stations covered by the ISMN is still growing, and approximately 70
   \% of the data sets contained in the database continue to be updated on
   a regular or irregular basis. The main scope of this paper is to inform
   readers about the evolution of the ISMN over the past decade, including
   a description of network and data set updates and quality control
   procedures. A comprehensive review of the existing literature making use
   of ISMN data is also provided in order to identify current limitations
   in functionality and data usage and to shape priorities for the next
   decade of operations of this unique community-based data repository.},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Dorigo, W (Corresponding Author), TU Wien, Dept Geodesy \& Geoinformat, Vienna, Austria.
   Dorigo, Wouter; Himmelbauer, Irene; Aberer, Daniel; Schremmer, Lukas; Petrakovic, Ivana; Zappa, Luca; Preimesberger, Wolfgang; Xaver, Angelika; Pfeil, Isabella; Vreugdenhil, Mariette; Wagner, Wolfgang, TU Wien, Dept Geodesy \& Geoinformat, Vienna, Austria.
   Annor, Frank, Delft Univ Technol, Trans African Hydrometeorol Observ, Delft, Netherlands.
   Annor, Frank; van de Giesen, Nick, Delft Univ Technol, Water Management Dept, Delft, Netherlands.
   Ardo, Jonas; Jensen, Karsten H.; Tagesson, Torbern, Lund Univ, Dept Phys Geog \& Ecosyst Sci, Lund, Sweden.
   Baldocchi, Dennis, Univ Calif Berkeley, Dept Environm Sci Policy \& Management, Berkeley, CA 94720 USA.
   Bitelli, Marco, Univ Bologna, Dept Agr \& Food Sci, Bologna, Italy.
   Bloeschl, Gunter, TU Wien, Inst Hydraul Engn \& Water Resources Management, Vienna, Austria.
   Bogena, Heye, Forschungszentrum Julich, Inst Bio \& Geosci Agrosphere IBG 3, Julich, Germany.
   Brocca, Luca, Natl Res Council Italy, Res Inst Geohydrol Protect, Perugia, Italy.
   Calvet, Jean-Christophe, Univ Toulouse, Meteo France, CNRS Ctr Natl Rech Sci, CNRM, Toulouse, France.
   Julio Camarero, J., IPE CSIC, Inst Pirenaico Ecol, Zaragoza, Spain.
   Capello, Giorgio, Natl Res Council Italy, Inst Sci \& Technol Sustainable Energy \& Mobil, Turin, Italy.
   Choi, Minha, Sungkyunkwan Univ, Coll Engn, Sch Civil Architectural \& Environm Engn, Environm \& Remote Sensing Lab, Suwon, Gyeonggi Do, South Korea.
   Cosh, Michael C., USDA ARS, Hydrol \& Remote Sensing Lab, Beltsville, MD USA.
   Hajdu, Istvan, PlantTech Res Inst, Tauranga, New Zealand.
   Ikonen, Jaakko, Finnish Meteorol Inst, Space \& Earth Observat Ctr, Helsinki, Finland.
   Jensen, Karsten H.; Tagesson, Torbern, Univ Copenhagen, Dept Geosci \& Nat Resource Management, Copenhagen, Denmark.
   Kanniah, Kasturi Devi, Univ Teknol Malaysia, Fac Built Environm \& Surveying, Ctr Environm Sustainabil \& Water Secur IPASA, Johor Baharu, Malaysia.
   de Kat, Ileen, VanderSat BV, Haarlem, Netherlands.
   Kirchengast, Gottfried, Karl Franzens Univ Graz, Wegener Ctr Climate \& Global Change WEGC, Graz, Austria.
   Rai, Pankaj Kumar, Invertis Univ, Dept Biotechnol, Bareilly, Uttar Pradesh, India.
   Kyrouac, Jenni; Sullivan, Ryan, Argonne Natl Lab, Environm Sci Div, Lemont, IL USA.
   Larson, Kristine, Univ Colorado, Dept Aerosp Engn Sci, Boulder, CO 80309 USA.
   Liu, Suxia, Chinese Acad Sci, Inst Geog Sci \& Nat Resources Res, Key Lab Water Cycle \& Related Land Surface Proc, Beijing, Peoples R China.
   Liu, Suxia, Univ Chinese Acad Sci, Sino Danish Ctr, Beijing, Peoples R China.
   Loew, Alexander, Ludwig Maximilians Univ Munchen, Dept Geog, Munich, Germany.
   Moghaddam, Mahta, Univ Southern Calif, Ming Hsieh Dept Elect \& Comp Engn, Los Angeles, CA 90007 USA.
   Martinez Fernandez, Jose, Univ Salamanca, Inst Hispano Luso Invest Agr, CIALE, Villamayor, Spain.
   Mattar Bader, Cristian, Univ Chile, Lab Anal Biosphere, Santiago, Chile.
   Morbidelli, Renato, Univ Perugia, Dept Civil \& Environm Engn, Perugia, Italy.
   Musial, Jan P., Inst Geodesy \& Cartog IGiK, Remote Sensing Ctr, Warsaw, Poland.
   Osenga, Elise, Aspen Global Change Inst AGCI, Basalt, CO USA.
   Palecki, Michael A., NOAA, Natl Ctr Environm Informat, Asheville, NC USA.
   Pellarin, Thierry, Univ Grenoble Alpes, LTHE, CNRS Ctr Natl Rech Sci, Grenoble, France.
   Petropoulos, George P., Harokopio Univ Athens, Dept Geog, Athens, Greece.
   Powers, Jarrett, Agr \& Agri Food Canada, Sci \& Technol Branch, Winnipeg, MB, Canada.
   Robock, Alan, Rutgers State Univ, Dept Environm Sci, New Brunswick, NJ USA.
   Rudiger, Christoph; Walker, Jeffrey, Monash Univ, Dept Civil Engn, Clayton, Vic, Australia.
   Rummel, Udo, DWD, Richard Assmann Observ, Meteorol Observ Lindenberg, Lindenberg, Germany.
   Strobel, Michael, USDA NRCS Natl Water \& Climate Ctr, Portland, OR USA.
   Su, Zhongbo; Zeng, Yijian, Univ Twente, Fac Geoinformat Sci \& Earth Observat, Enschede, Netherlands.
   Varlagin, Andrej, Russian Acad Sci, AN Severtsov Inst Ecol \& Evolut, Moscow, Russia.
   Wen, Jun, Chengdu Univ Informat Technol, Plateau Atmosphere \& Environm Key Lab Sichuan Pro, Coll Atmospher Sci, Chengdu, Peoples R China.
   Wenger, Fred, Norwegian Water Resources \& Energy Directorate, Oslo, Norway.
   Wigneron, Jean Pierre, INRAE Bordeaux Aquitaine, ISPA, MOST, Bordeaux, France.
   Woods, Mel, Univ Dundee, Duncan Jordanstone Coll Art \& Design, Social Digital, Dundee, Scotland.
   Yang, Kun, Tsinghua Univ, Dept Earth Syst Sci, Beijing, Peoples R China.
   Zhang, Xiang, Wuhan Univ, State Key Lab Informat Engn Surveying Mapping \& R, Wuhan, Peoples R China.
   Zreda, Marek, Univ Arizona, Dept Hydrol \& Atmospher Sci, Tucson, AZ USA.
   Dietrich, Stephan, Fed Inst Hydrol, Int Ctr Water Resources \& Global Change ICWRGC UN, Koblenz, Germany.
   Gruber, Alexander, Katholieke Univ Leuven, Dept Earth \& Environm Sci, Heverlee, Belgium.
   van Oevelen, Peter, Int GEWEX Project Off, Washington, DC USA.
   Scipal, Klaus; Sabia, Roberto, European Space Agcy, ESRIN, Frascati, Italy.
   Drusch, Matthias, European Space Agcy, ESTEc, Noordwijk, Netherlands.},
DOI = {10.5194/hess-25-5749-2021},
ISSN = {1027-5606},
EISSN = {1607-7938},
Keywords-Plus = {LAND DATA ASSIMILATION; WIRELESS SENSOR NETWORK; ANTECEDENT WETNESS
   CONDITIONS; SMOS BRIGHTNESS TEMPERATURE; IN-SITU MEASUREMENTS;
   CONSECUTIVE DRY DAYS; HEIHE RIVER-BASIN; LEAF-AREA INDEX; AMSR-E;
   SPATIAL VARIABILITY},
Research-Areas = {Geology; Water Resources},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary; Water Resources},
Author-Email = {wouter.dorigo@tuwien.ac.at},
Affiliations = {Technische Universitat Wien; Delft University of Technology; Delft
   University of Technology; Lund University; University of California
   System; University of California Berkeley; University of Bologna;
   Technische Universitat Wien; Helmholtz Association; Research Center
   Julich; Consiglio Nazionale delle Ricerche (CNR); Meteo France;
   Universite de Toulouse; Consejo Superior de Investigaciones Cientificas
   (CSIC); CSIC - Instituto Pirenaico de Ecologia (IPE); Consiglio
   Nazionale delle Ricerche (CNR); Sungkyunkwan University (SKKU); United
   States Department of Agriculture (USDA); Finnish Meteorological
   Institute; University of Copenhagen; Universiti Teknologi Malaysia;
   University of Graz; Invertis University; United States Department of
   Energy (DOE); Argonne National Laboratory; University of Colorado
   System; University of Colorado Boulder; Chinese Academy of Sciences;
   Institute of Geographic Sciences \& Natural Resources Research, CAS;
   Chinese Academy of Sciences; University of Chinese Academy of Sciences,
   CAS; University of Munich; University of Southern California; University
   of Salamanca; Universidad de Chile; University of Perugia; National
   Oceanic Atmospheric Admin (NOAA) - USA; Communaute Universite Grenoble
   Alpes; Institut National Polytechnique de Grenoble; Universite Grenoble
   Alpes (UGA); Centre National de la Recherche Scientifique (CNRS);
   Institut de Recherche pour le Developpement (IRD); Harokopio University
   Athens; Agriculture \& Agri Food Canada; Rutgers System; Rutgers New
   Brunswick; Monash University; Deutscher Wetterdienst; University of
   Twente; Russian Academy of Sciences; Saratov Scientific Center of the
   Russian Academy of Sciences; Severtsov Institute of Ecology \&
   Evolution; Chengdu University of Information Technology; Norwegian Water
   Resources \& Energy Directorate; INRAE; University of Dundee; Tsinghua
   University; Wuhan University; University of Arizona; KU Leuven; European
   Space Agency; European Space Agency},
ResearcherID-Numbers = {van de Giesen, Nick/B-5010-2008
   Bogena, Heye/AAD-5653-2022
   Jensen, Karsten H/E-3469-2015
   Tagesson, Torbern/AGG-5627-2022
   Martinez-Fernandez, Jose/B-3877-2012
   Baldocchi, Dennis D./A-1625-2009
   Kirchengast, Gottfried/D-4990-2016
   Petropoulos, George P./N-5810-2019
   Su, Z./D-4383-2009
   Varlagin, Andrej/A-6568-2012
   yang, kun/JGM-4169-2023
   Wagner, Wolfgang/AAC-5507-2019
   Calvet, Jean-Christophe/A-8762-2012
   Wigneron, Jean-Pierre André/ABD-9939-2021
   zeng, yijian/C-1207-2008
   Yang, Kun/G-8390-2011
   Morbidelli, Renato/AAT-7106-2021
   Robock, Alan/B-6385-2016
   Choi, Minha/ABH-7266-2020
   Camarero, J. Julio/A-8602-2013
   Brocca, Luca/F-2854-2010
   Dorigo, Wouter/C-7794-2014
   },
ORCID-Numbers = {van de Giesen, Nick/0000-0002-7200-3353
   Bogena, Heye/0000-0001-9974-6686
   Jensen, Karsten H/0000-0003-4020-0050
   Martinez-Fernandez, Jose/0000-0003-0446-9693
   Baldocchi, Dennis D./0000-0003-3496-4919
   Kirchengast, Gottfried/0000-0001-9187-937X
   Petropoulos, George P./0000-0003-1442-1423
   Varlagin, Andrej/0000-0002-2549-5236
   Wagner, Wolfgang/0000-0001-7704-6857
   Calvet, Jean-Christophe/0000-0001-6425-6492
   Wigneron, Jean-Pierre André/0000-0001-5345-3618
   zeng, yijian/0000-0002-2166-5314
   Yang, Kun/0000-0002-0809-2371
   Camarero, J. Julio/0000-0003-2436-2922
   Brocca, Luca/0000-0002-9080-260X
   Woods, Mel/0000-0002-5507-0976
   Vreugdenhil, Mariette/0000-0003-4913-0255
   Rai, Pankaj/0000-0002-4962-7635
   Zappa, Luca/0000-0002-0928-229X
   Dorigo, Wouter/0000-0001-8054-7572
   Musial, Jan/0000-0002-0034-7827
   Ardo, Jonas/0000-0002-9318-0973
   Gruber, Alexander/0000-0002-3280-7023
   Capello, Giorgio/0000-0001-6993-8513
   Preimesberger, Wolfgang/0000-0002-6655-0588
   Su, Zhongbo/0000-0003-2096-1733},
Funding-Acknowledgement = {SMOSnet International Soil Moisture Network {[}4000102722/10/NL/FF/fk];
   IDEAS C {[}TVUK/AG/18/02082]; QA4EO {[}TPZV/UK/AG/19/02321]; QA4SM
   {[}4000135204/21//I-BG]; EU FP7 EartH2Observe project {[}603608]; EU
   H2020 GROW project {[}690199]; Austrian Space Applications Programme
   {[}866004]; TWIGA {[}776691]; Russian Foundation for Basic Research
   {[}19-04-01234-a]; TU Wien Bibliothek;  {[}3-13185/NL/FF/fk]; 
   {[}FWO-1224320N];  {[}FWO-1530019N]; H2020 Societal Challenges Programme
   {[}690199] Funding Source: H2020 Societal Challenges Programme},
Funding-Text = {The authors greatly acknowledge the financial support provided by ESA
   through various projects including the following: SMOSnet International
   Soil Moisture Network (grant no. 4000102722/10/NL/FF/fk) and Operations
   (grant no. 3-13185/NL/FF/fk), IDEAS C (grant no. TVUK/AG/18/02082),
   QA4EO (grant no. TPZV/UK/AG/19/02321), and QA4SM (grant no.
   4000135204/21//I-BG). Additional funding for the methodological advances
   has been received from the EU FP7 EartH2Observe project (grant no.
   603608), the EU H2020 GROW project (grant no. 690199), and the QA4SM
   project funded by the Austrian Space Applications Programme 14 (grant
   no. 866004). Network funding has been provided by TWIGA (grant no.
   776691). Andrej Varlagin has been supported by the Russian Foundation
   for Basic Research (grant no. 19-04-01234-a). Alexander Gruber also
   received funding (grant nos. FWO-1224320N and FWO-1530019N). TU Wien
   Bibliothek has provided financial support through its open-access
   funding programme.},
Number-of-Cited-References = {450},
Times-Cited = {107},
Usage-Count-Last-180-days = {18},
Usage-Count-Since-2013 = {132},
Journal-ISO = {Hydrol. Earth Syst. Sci.},
Doc-Delivery-Number = {WU3PD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000716459500001},
OA = {Green Submitted, gold, Green Published, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000431447200001,
Author = {Kaufman, Darrell S. and PAGES 2k special-issue editorial},
Title = {Technical note: Open-paleo-data implementation pilot - the PAGES 2k
   special issue},
Journal = {CLIMATE OF THE PAST},
Year = {2018},
Volume = {14},
Number = {5},
Pages = {593-600},
Month = {MAY 3},
Abstract = {Data stewardship is an essential element of the publication process.
   Knowing how to enact data polices that are described only in general
   terms can be difficult, however. Examples are needed to model the
   implementation of opendata polices in actual studies. Here we explain
   the procedure used to attain a high and consistent level of data
   stewardship across a special issue of the journal Climate of the Past.
   We discuss the challenges related to (1) determining which data are
   essential for public archival, (2) using data generated by others, and
   (3) understanding data citations. We anticipate that open-data sharing
   in paleo sciences will accelerate as the advantages become more evident
   and as practices that reduce data loss become the accepted convention.},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Kaufman, DS (Corresponding Author), No Arizona Univ, Sch Earth Sci \& Environm Sustainabil, Flagstaff, AZ 86011 USA.
   Kaufman, Darrell S., No Arizona Univ, Sch Earth Sci \& Environm Sustainabil, Flagstaff, AZ 86011 USA.},
DOI = {10.5194/cp-14-593-2018},
ISSN = {1814-9324},
EISSN = {1814-9332},
Keywords-Plus = {SCIENCE},
Research-Areas = {Geology; Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary; Meteorology \& Atmospheric Sciences},
Author-Email = {darrell.kaufman@nau.edu},
Affiliations = {Northern Arizona University},
ResearcherID-Numbers = {Kaufman, Darrell S/A-2471-2008
   Martrat, Belen/I-5952-2015
   Linderholm, Hans W/N-1020-2013
   McGregor, Helen/I-1479-2013
   },
ORCID-Numbers = {Kaufman, Darrell S/0000-0002-7572-1414
   Martrat, Belen/0000-0001-9904-9178
   Linderholm, Hans W/0000-0002-1522-8919
   McGregor, Helen/0000-0002-4031-2282
   Evans, Michael Neil/0000-0003-3727-6898
   Abram, Nerilie/0000-0003-1246-2344
   St. George, Scott/0000-0002-0945-4944
   von Gunten, Lucien/0000-0003-0425-2881},
Funding-Acknowledgement = {US National Science Foundation; Swiss Academy of Sciences; ARC; 
   {[}NSF-AGS-1602105]; Div Atmospheric \& Geospace Sciences; Directorate
   For Geosciences {[}1602105] Funding Source: National Science Foundation;
   Division Of Earth Sciences; Directorate For Geosciences {[}1440015]
   Funding Source: National Science Foundation},
Funding-Text = {We thank the authors of the PAGES 2k special issue, Copernicus
   Publications, and the paleo-data repositories, who worked with us to
   develop practices to help reduce the loss of valued data. We are
   grateful to those who reviewed an earlier version of the paper and
   contributed to the frank debate in the interactive discussion, including
   its spin-offs on social media. This paper is a contribution to the Past
   Global Changes (PAGES) Data Stewardship Integrative Activity. PAGES is
   supported by the US National Science Foundation, and the Swiss Academy
   of Sciences. Helen V. McGregor and Nerilie J. Abram are supported by ARC
   Future Fellowships. Darrell S. Kaufman is funded by NSF-AGS-1602105.},
Number-of-Cited-References = {28},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Clim. Past.},
Doc-Delivery-Number = {GE7XU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000431447200001},
OA = {gold, Green Published, Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000962786500001,
Author = {Duncan, Alan J. and Lukuyu, Ben and Mutoni, Gilbert and Lema, Zelalem
   and Fraval, Simon},
Title = {Supporting participatory livestock feed improvement using the Feed
   Assessment Tool (FEAST)},
Journal = {AGRONOMY FOR SUSTAINABLE DEVELOPMENT},
Year = {2023},
Volume = {43},
Number = {2},
Month = {APR},
Abstract = {Livestock production is central to the livelihoods of smallholder
   farmers in low- and middle-income countries, but livestock are often
   poorly fed which limits their potential for reducing poverty. Efforts to
   improve livestock nutrition are often driven by supply-push thinking and
   fail to engage meaningfully with farmers and the realities they face.
   The Feed Assessment Tool (FEAST) was developed as a way of involving
   farmers more closely in decision making on livestock feed improvement.
   FEAST is a participatory tool which uses focus group discussions and
   individual farmer interviews to develop a broad overview of the
   livestock farming system. FEAST has been applied in many countries in
   the last 10 years. Examples of intensive use come from the Accelerated
   Value Chain Development Project in Kenya and the Rwanda Dairy
   Development Project in Rwanda. In both cases the tool was used to inform
   feed options with strong input from farmers. Although the primary
   purpose of FEAST is to support improved feed strategies at farm level,
   the data collected through the FEAST app and published in FEAST reports
   are a rich information resource that can be useful for developing
   broader system-level understanding of livestock feed issues. FEAST data
   can be uploaded into a global data repository where they are available
   for researchers. These data are also used to generate visualizations of
   key feed metrics further extending the use of secondary data. FEAST is
   an example of a participatory tool that moves decision making in the
   direction of farmers, while providing insights to researchers working
   across farming systems. Its widespread use across many countries is an
   indication that it fills a gap in in the livestock feed development
   space. Its novelty lies in bridging the knowledge gap (both ways)
   between livestock researchers and small-scale livestock keepers.},
Publisher = {SPRINGER FRANCE},
Address = {22 RUE DE PALESTRO, PARIS, 75002, FRANCE},
Type = {Article},
Language = {English},
Affiliation = {Duncan, AJ (Corresponding Author), Int Livestock Res Inst, POB 5689, Addis Ababa, Ethiopia.
   Duncan, AJ (Corresponding Author), Univ Edinburgh, Global Acad Agr \& Food Syst, Royal Dick Sch Vet Studies, Edinburgh EH25 9RG, Midlothian, Scotland.
   Duncan, AJ (Corresponding Author), Univ Edinburgh, Roslin Inst, Easter Bush Campus, Edinburgh EH25 9RG, Midlothian, Scotland.
   Duncan, Alan J.; Lukuyu, Ben; Mutoni, Gilbert, Int Livestock Res Inst, POB 5689, Addis Ababa, Ethiopia.
   Duncan, Alan J.; Fraval, Simon, Univ Edinburgh, Global Acad Agr \& Food Syst, Royal Dick Sch Vet Studies, Edinburgh EH25 9RG, Midlothian, Scotland.
   Duncan, Alan J.; Fraval, Simon, Univ Edinburgh, Roslin Inst, Easter Bush Campus, Edinburgh EH25 9RG, Midlothian, Scotland.
   Lema, Zelalem, Univ New England, Sch Environm \& Rural Sci, Armidale, NSW 2351, Australia.},
DOI = {10.1007/s13593-023-00886-9},
Article-Number = {34},
ISSN = {1774-0746},
EISSN = {1773-0155},
Keywords = {Participatory tools; Livestock; Systems; Data; Smallholder; Livestock
   feed},
Keywords-Plus = {SYSTEMS; INNOVATION; LESSONS},
Research-Areas = {Agriculture; Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Agronomy; Green \& Sustainable Science \& Technology},
Author-Email = {a.duncan@cgiar.org},
Affiliations = {CGIAR; International Livestock Research Institute (ILRI); University of
   Edinburgh; University of Edinburgh; UK Research \& Innovation (UKRI);
   Biotechnology and Biological Sciences Research Council (BBSRC); Roslin
   Institute; University of New England},
ResearcherID-Numbers = {Moti, Zelalem Lema/J-2350-2015
   Duncan, Alan/A-1788-2013},
ORCID-Numbers = {Moti, Zelalem Lema/0000-0001-9275-8828
   Duncan, Alan/0000-0002-3954-3067},
Funding-Acknowledgement = {International Fund for Agricultural Development (IFAD); USAID;
   Government of Rwanda; CGIAR Trust Fund.},
Funding-Text = {The development of the FEAST tool has been supported by multiple
   projects but notably by the International Fund for Agricultural
   Development (IFAD). The Advancing Value Chain Development Project was
   funded by USAID. ILRI's technical support to the Rwanda Dairy
   Development Program was supported by Government of Rwanda through a loan
   made by IFAD. We thank all partners and donors that globally support our
   work through their contributions to the CGIAR system and in particular
   to the Livestock CRP (http://www.cgiar.org/about-us/our-funders).
   Latterly, this work/research was conducted as part of the CGIAR
   Initiative on Sustainable Animal Productivity which is supported by
   contributors to the CGIAR Trust Fund. For the purpose of open access,
   the author has applied a Creative Commons Attribution (CC BY) license to
   any Author Accepted Manuscript version arising from this submission.},
Number-of-Cited-References = {44},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Agron. Sustain. Dev.},
Doc-Delivery-Number = {C6CZ2},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000962786500001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000540908900014,
Author = {Al-Sharabi, Mohammed and Markl, Daniel and Mudley, Theona and Bawuah,
   Prince and Karttunen, Anssi-Pekka and Ridgway, Cathy and Gane, Patrick
   and Ketolainen, Jarkko and Peiponen, Kai-Erik and Rades, Thomas and
   Zeitler, J. Axel},
Title = {Simultaneous investigation of the liquid transport and swelling
   performance during tablet disintegration},
Journal = {INTERNATIONAL JOURNAL OF PHARMACEUTICS},
Year = {2020},
Volume = {584},
Month = {JUN 30},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Zeitler, JA (Corresponding Author), Univ Cambridge, Dept Chem Engn \& Biotechnol, Cambridge CB3 0AS, England.
   Al-Sharabi, Mohammed; Mudley, Theona; Bawuah, Prince; Zeitler, J. Axel, Univ Cambridge, Dept Chem Engn \& Biotechnol, Cambridge CB3 0AS, England.
   Markl, Daniel, Univ Strathclyde, Strathclyde Inst Pharm \& Biomed Sci, 161 Cathedral St, Glasgow G4 0RE, Lanark, Scotland.
   Markl, Daniel, Univ Strathclyde, EPSRC Ctr Innovat Mfg Continuous Mfg \& Crystallis, 99 George St, Glasgow G1 1RD, Lanark, Scotland.
   Karttunen, Anssi-Pekka; Ketolainen, Jarkko, Univ Eastern Finland, Promis Ctr, Sch Pharm, POB 1627, FI-70211 Kuopio, Finland.
   Ridgway, Cathy, Omya Int AG, Forschackerstr 6, CH-4622 Egerkingen, Switzerland.
   Gane, Patrick, Aalto Univ, Sch Chem Engn, Dept Bioprod \& Biosyst, FI-00076 Aalto, Finland.
   Peiponen, Kai-Erik, Univ Eastern Finland, Inst Photon, POB 111, FI-80101 Joensuu, Finland.
   Rades, Thomas, Univ Copenhagen, Dept Pharm, Univ Pk 2, DK-2100 Copenhagen, Denmark.},
DOI = {10.1016/j.ijpharm.2020.119380},
Article-Number = {119380},
ISSN = {0378-5173},
EISSN = {1873-3476},
Keywords-Plus = {PHARMACEUTICAL TABLETS; IMMEDIATE-RELEASE; PORE STRUCTURE;
   MICROCRYSTALLINE CELLULOSE; POWDERED PREPARATIONS; DIRECT COMPRESSION;
   TASTE-MASKING; TIME; WATER; POROSITY},
Research-Areas = {Pharmacology \& Pharmacy},
Web-of-Science-Categories  = {Pharmacology \& Pharmacy},
Author-Email = {jaz22@cam.ac.uk},
Affiliations = {University of Cambridge; University of Strathclyde; UK Research \&
   Innovation (UKRI); Engineering \& Physical Sciences Research Council
   (EPSRC); University of Strathclyde; University of Eastern Finland; Omya
   International AG; Aalto University; University of Eastern Finland;
   University of Copenhagen},
ResearcherID-Numbers = {Rades, Thomas/ABE-9953-2021
   Zeitler, Axel/B-4885-2008
   Markl, Daniel/I-3436-2019
   },
ORCID-Numbers = {Rades, Thomas/0000-0002-7521-6020
   Zeitler, Axel/0000-0002-4958-0582
   Markl, Daniel/0000-0003-0411-733X
   Karttunen, Anssi-Pekka/0000-0002-4286-2384
   Al-Sharabi, Mohammed/0000-0001-5442-3373},
Funding-Acknowledgement = {U.K. Engineering and Physical Sciences Research Council (EPSRC); Omya
   International AG; EPSRC {[}EP/P006965/1, 1943009] Funding Source: UKRI},
Funding-Text = {We would like to thank Johnson Matthey and the U.K. Engineering and
   Physical Sciences Research Council (EPSRC) for their funding, and Omya
   International AG for providing the FCC and performing the surface area
   and porosimetric analyses. The raw data that was used to prepare the
   figures in this manuscript can be downloaded from the University of
   Cambridge Open Data Repository at https://doi.org/10.17863/CAM.52591.},
Number-of-Cited-References = {54},
Times-Cited = {25},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {14},
Journal-ISO = {Int. J. Pharm.},
Doc-Delivery-Number = {LZ0GA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000540908900014},
OA = {Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000654510000017,
Author = {Sun, Lingzhi and Lucey, Paul G. and Taylor, G. Jeffrey},
Title = {Correlating Apollo Soil Mineralogical Data With Kaguya Spectral Data for
   a Global Mineralogical Classification},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-PLANETS},
Year = {2021},
Volume = {126},
Number = {5},
Month = {MAY},
Abstract = {Although lunar soils contain rock and mineral components from the
   breakdown of a mixture of rock types, a classification based on the
   abundances of the major silicate minerals plagioclase, olivine, low-Ca
   pyroxene (LCP) and high-Ca pyroxene can be used to evaluate the major
   compositional classes that are represented within a given soil. We
   studied the compositional classes for Apollo 15, 16, and 17 soil samples
   based on the mineral modal abundances derived by X-ray diffraction
   (XRD). Using the XRD results as a ground truth, we determined the
   compositional classes of the Apollo 15, 16, and 17 sampling stations
   using mineral maps from the Kaguya Multiband Imager (MI), then mapped
   areas having compositional classes similar to the sampling stations on
   regional and global scales. Global distribution of compositional classes
   was also mapped using MI mineral maps, and the major compositional
   classes of lunar nonmare surfaces are noritic anorthosite (40\%),
   anorthositic norite (24\%), and anorthosite (23\%). Our maps show that
   the lunar highlands and the South Pole-Aitken (SPA) basin are enriched
   with noritic materials, indicating the widespread occurrence of LCP-rich
   and olivine-poor assemblages. In contrast to the SPA basin and the
   highlands, the basin rings of Serenitatis, Crisium, Humorum, Nectaris,
   Orientale, and Hertzsprung exhibit higher olivine/pyroxene ratios (>2),
   and we interpret this signature as reflecting a contribution from
   olivine-rich upper mantle components.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Sun, LZ (Corresponding Author), Univ Hawaii Manoa, Dept Earth Sci, Hawaii Inst Geophys \& Planetol, Honolulu, HI 96822 USA.
   Sun, Lingzhi; Lucey, Paul G.; Taylor, G. Jeffrey, Univ Hawaii Manoa, Dept Earth Sci, Hawaii Inst Geophys \& Planetol, Honolulu, HI 96822 USA.},
DOI = {10.1029/2020JE006445},
Article-Number = {e2020JE006445},
ISSN = {2169-9097},
EISSN = {2169-9100},
Keywords = {Apollo soils; lunar remote sensing; mineralogical classification; XRD},
Keywords-Plus = {CENTRAL-HIGHLANDS; MODAL ANALYSES; BASIN EJECTA; LUNAR; MANTLE; HISTORY;
   CRUST; ROCK; BRECCIAS; MOON},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {lzsun@higp.hawaii.edu},
Affiliations = {University of Hawaii System; University of Hawaii Manoa},
ORCID-Numbers = {Sun, Lingzhi/0000-0002-6985-1992
   Lucey, Paul/0000-0002-4959-2495},
Funding-Acknowledgement = {NASA's Planetary Data Archiving, Restoration and Tools; Lunar Data
   Analysis programs; NASA LASER program {[}NNX11AE85G]; NASA
   {[}NNX11AE85G, 147706] Funding Source: Federal RePORTER},
Funding-Text = {We thank Dr. Daniel Moriarty and Dr. Bradley Jolliff whose comments and
   suggestions helped improve and clarify this manuscript. This work was
   supported in part by the NASA's Planetary Data Archiving, Restoration
   and Tools and the Lunar Data Analysis programs. The lunar soil XRD
   measurements were funded by the NASA LASER program (grant NNX11AE85G),
   and mineral modal abundances are available at the Open Data Repository:
   https://odr.io/lunar-regolith-xrd.},
Number-of-Cited-References = {93},
Times-Cited = {5},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {9},
Journal-ISO = {J. Geophys. Res.-Planets},
Doc-Delivery-Number = {SI0HT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000654510000017},
DA = {2024-01-15},
}

@article{ WOS:000464922800053,
Author = {Birren, T. and Reber, J. E.},
Title = {The Impact of Rheology on the Transition From Stick-Slip to Creep in a
   Semibrittle Analog},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH},
Year = {2019},
Volume = {124},
Number = {3},
Pages = {3144-3154},
Month = {MAR},
Abstract = {Faults can release energy via a variety of different slip mechanisms
   ranging from steady creep to fast and destructive earthquakes. Tying the
   rheology of the crust to various slip dynamics is important for our
   understanding of plate tectonics and earthquake generation. Here we
   propose that the interplay of fractures and viscous flow leads to a
   spectrum between stick-slip and creep. We use an elasto-visco-plastic
   rock analog (Carbopol U-21) where we vary the yield stress to
   investigate its impact on slip dynamics in shear experiments. The
   experiments are performed using a simple shear apparatus, which provides
   distributed shear across the entire width of the experiment and allows
   in situ observations of deformation. We record force and displacement
   during deformation and use time lapse photography to document fracture
   development. A low yield stress (25Pa) leads to creep dynamics in the
   absence of fractures. An intermediate yield stress (144Pa) leads to the
   development and interaction of opening (mode I) and shear (mode II)
   fractures. This interaction leads to a spectrum in slip dynamics ranging
   from creep to stick-slip. A high yield stress (357Pa) results in the
   development of many mode I fractures and a deformation signal dominated
   by stick-slip. These results show that bulk yield stress, fracture
   formation, and slip dynamics are closely linked and can lead to a
   continuum between creep and stick-slip. We suggest that rheology should
   be considered as an additional mechanism to explain the broad range of
   slip dynamics in natural faults.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Birren, T (Corresponding Author), Iowa State Univ, Dept Geol \& Atmospher Sci, Ames, IA 50011 USA.
   Birren, T.; Reber, J. E., Iowa State Univ, Dept Geol \& Atmospher Sci, Ames, IA 50011 USA.},
DOI = {10.1029/2018JB016914},
ISSN = {2169-9313},
EISSN = {2169-9356},
Keywords = {slip dynamics; Carbopol; semibrittle; analog experiments},
Keywords-Plus = {LOW METAMORPHIC GRADE; BRITTLE-FRACTURE; DEFORMATION; DUCTILE; FLOW;
   EARTHQUAKES; GRANITOIDS; SUBDUCTION; FAULT; LOCALIZATION},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {tbirren@iastate.edu},
Affiliations = {Iowa State University},
ORCID-Numbers = {Birren, Thomas/0000-0002-5603-458X},
Funding-Acknowledgement = {NSF {[}EAR-1547492]},
Funding-Text = {We thank Neil Mancktelow and Alexandra Hatem for their thoughtful
   comments and helpful suggestions. T.B. and J.E.R. were supported by NSF
   grant EAR-1547492. Special thanks to Kevin Toeneboehn and Michele Cooke
   for help in developing Matlab codes for use in this study. Data
   presented in the results and supplemental information is freely
   available through DataShare: the Open Data Repository of Iowa State
   University (https://doi.org/10.25380/iastate.7746635).},
Number-of-Cited-References = {43},
Times-Cited = {9},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {8},
Journal-ISO = {J. Geophys. Res.-Solid Earth},
Doc-Delivery-Number = {HT9WG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000464922800053},
OA = {Green Published, Bronze},
DA = {2024-01-15},
}

@article{ WOS:001066253600001,
Author = {Koesters, Wolf Iring and Hoerner, Stefan},
Title = {Simultaneous flow measurement and deformation tracking for passive flow
   control experiments involving fluid-structure interactions},
Journal = {JOURNAL OF FLUIDS AND STRUCTURES},
Year = {2023},
Volume = {121},
Month = {AUG},
Abstract = {Fluid-structure interactions (FSI) on highly flexible structures involve
   large deformations and require specific techniques for a thorough
   investigation of the flow field and structural deformation. To this
   purpose, a physics-informed method is introduced that allows for
   simultaneous determination of the flow fields and the structural
   deformation by using Particle Image Velocimetry (PIV) raw images. The
   method combines apriori knowledge of the mechanical characteristics of
   the flexible structure with classical image processing techniques for
   segmentation. PIV recordings of an actively pitched, highly deformable
   hydrodynamic profile experiment in a closed water tunnel serve as an
   example case. To achieve accurate results, the contour obtained from
   image segmentation is further defined under the assumption that its
   flexure can be described with the Euler-Bernoulli beam theory model.
   This makes it possible to determine the neutral fiber of the structure
   and the final reconstruction becomes possible from knowledge of the
   original geometry. The resulting procedure allows for a recognition of
   the structure itself and is suitable for cross-section deformation
   measurements and for masking of the structure in the raw images to
   improve the PIV processing. A test case comprising synthetic data
   similar to the application with a modeled profile geometry of known
   shape is used to investigate the accuracy of the method and its validity
   for deformation measurements. Under conditions of cyclic dynamic stall,
   a mean absolute error of 0.84 \& DEG; could be reached, with a
   deterioration up to 2 \& DEG; mean absolute error under static stall.
   The method has a major advantage compared to other technically more
   sophisticated and complex methods, such as the combination of Laser
   interferometers combined with Laser-Doppler Anemometry: the method
   allows for the usage of a single data source for both, fluid and solid
   in a unified measurement method. Therefore a direct comparison of
   instantaneous flow field and deformation is possible. In consequence it
   is in particular useful for highly dynamic multi-physical processes
   involving extreme deformations, such as passive flow control and soft
   actuated or flexible under water robotics. \& COPY; 2023 The Author(s).
   Published by Elsevier Ltd. This is an open access article under the CC
   BY license (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD},
Address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Kösters, WI (Corresponding Author), Otto von Guericke Univ Magdeburg OvGU, Inst Fluid Dynam \& Thermodynam, Lab Fluid Dynam \& Tech Flows, Univ Pl 2, D-39106 Magdeburg, Germany.
   Koesters, Wolf Iring; Hoerner, Stefan, Otto von Guericke Univ Magdeburg OvGU, Inst Fluid Dynam \& Thermodynam, Lab Fluid Dynam \& Tech Flows, Univ Pl 2, D-39106 Magdeburg, Germany.
   Koesters, Wolf Iring, Tallinn Univ Technol Taltech, Ctr Biorobot, Akad Tee 15A, EE-12616 Tallinn, Estonia.},
DOI = {10.1016/j.jfluidstructs.2023.103956},
EarlyAccessDate = {AUG 2023},
Article-Number = {103956},
ISSN = {0889-9746},
EISSN = {1095-8622},
Keywords = {Fluid-structure interaction; Deformation tracking; PIV; Masking;
   NACA0018 hydrofoil; Passive flow control},
Keywords-Plus = {PIV; HYDRODYNAMICS; TURBINES; IMAGES},
Research-Areas = {Engineering; Mechanics},
Web-of-Science-Categories  = {Engineering, Mechanical; Mechanics},
Author-Email = {wolf.koesters@ovgu.de},
Affiliations = {Otto von Guericke University; Tallinn University of Technology},
ORCID-Numbers = {Hoerner, Stefan/0000-0001-9167-4964},
Funding-Acknowledgement = {European Union {[}860108]},
Funding-Text = {The authors thank Christian-Toralf Weber and Carsten Laddey (University
   of Applied Sciences Magdeburg) for providing the foundation for image
   material from structural mechanics analysis of the hydrofoil. The
   authors are grateful to Cyrille Bonamy and Pierre Augier (LEGI) for
   their work and their assistance regarding the incorporation of the PIV
   framework ``FluidImage{''}into the workflow. Olivier Cleynen is thanked
   for language editing and commenting on the first manuscript of this
   article. The authors are grateful to the open science team of the
   University Magdeburg for their data repository services. This project is
   part of the EU Marie Curie International Training Network on Soft,
   Self-responsive, Smart Materials for Robots (SMART-ITN) and has received
   funding from the European Union's Horizon 2020 research and innovation
   program under the Marie Sklodowska-Curie grant agreement No 860108.},
Number-of-Cited-References = {50},
Times-Cited = {0},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {2},
Journal-ISO = {J. Fluids Struct.},
Doc-Delivery-Number = {R7QB9},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001066253600001},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000857079000007,
Author = {Amorosino, Gabriele and Peruzzo, Denis and Redaelli, Daniela and
   Olivetti, Emanuele and Arrigoni, Filippo and Avesani, Paolo},
Title = {DBB - A Distorted Brain Benchmark for Automatic Tissue Segmentation in
   Paediatric Patients},
Journal = {NEUROIMAGE},
Year = {2022},
Volume = {260},
Month = {OCT 15},
Abstract = {T1 -weighted magnetic resonance images provide a comprehensive view of
   the morphology of the human brain at the macro scale. These images are
   usually the input of a segmentation process that aims detecting the
   anatomical structures labeling them according to a predefined set of
   target tissues. Automated methods for brain tissue segmentation rely on
   anatomical priors of the human brain structures. This is the reason why
   their performance is quite accurate on healthy individuals. Nevertheless
   model-based tools become less accurate in clinical practice,
   specifically in the cases of severe lesions or highly distorted cerebral
   anatomy. More recently there are empirical evidences that a data-driven
   approach can be more robust in presence of alterations of brain
   structures, even though the learning model is trained on healthy brains.
   Our contribution is a benchmark to support an open investigation on how
   the tissue segmentation of distorted brains can be improved by adopting
   a supervised learning approach. We formulate a precise definition of the
   task and propose an evaluation metric for a fair and quantitative
   comparison. The training sample is composed of almost one thousand
   healthy individuals. Data include both Tl-weighted MR images and their
   labeling of brain tissues. The test sample is a collection of several
   tens of individuals with severe brain distortions. Data and code are
   openly published on Brain-Life, an open science platform for
   reproducible neuroscience data analysis.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Amorosino, G (Corresponding Author), Bruno Kessler Fdn FBK, NeuroInformat Lab NILab, Trento, Italy.
   Amorosino, Gabriele; Olivetti, Emanuele; Avesani, Paolo, Bruno Kessler Fdn FBK, NeuroInformat Lab NILab, Trento, Italy.
   Amorosino, Gabriele; Olivetti, Emanuele; Avesani, Paolo, Univ Trento, Ctr Mind \& Brain Sci CIMeC, Trento, Italy.
   Peruzzo, Denis, Sci Inst IRCCS Eugenio Medea, Neuroimaging Lab, Bosisio Parini, Italy.
   Redaelli, Daniela, Fatebenefratelli Hosp, Radiol Unit, Milan, Italy.
   Arrigoni, Filippo, V Buzzi Childrens Hosp, Paediat Radiol \& Neuroradiol Dept, Milan, Italy.},
DOI = {10.1016/j.neuroimage.2022.119486},
EarlyAccessDate = {JUL 2022},
Article-Number = {119486},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords = {Brain tissue segmentation; Brain malformation; Machine learning;
   Supervised learning; Benchmark; Magnetic resonance imaging (MRI)},
Keywords-Plus = {IMAGE SEGMENTATION; MRI; PERFORMANCE; CONTRAST; ANTS},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {gamorosino@fbk.eu},
Affiliations = {Fondazione Bruno Kessler; University of Trento; IRCCS Eugenio Medea},
ResearcherID-Numbers = {ARRIGONI, FILIPPO/G-5828-2011
   Amorosino, Gabriele/AAB-2804-2022
   Olivetti, Emanuele/AAT-2384-2020
   Avesani, Paolo/AAY-9704-2021
   Peruzzo, Denis/K-3356-2015},
ORCID-Numbers = {ARRIGONI, FILIPPO/0000-0002-5508-1149
   Amorosino, Gabriele/0000-0003-2789-5193
   Olivetti, Emanuele/0000-0001-7653-1519
   Avesani, Paolo/0000-0001-8943-8911
   Peruzzo, Denis/0000-0002-9480-379X},
Funding-Acknowledgement = {National Institute of Child Health and Human Development
   {[}HHSN275200900018C]; National Institute of Child Health and Human
   Development; National Institute on Drug Abuse; National Institute of
   Mental Health; National Institute of Neurological Disorders and Stroke
   {[}N01-HD02-3343, N01-MH90002, N01-NS-9-2314, N01-NS-9-2315,
   N01-NS-9-2316, N01-NS-9-2317, N01-NS-9-2319, N01-NS-9-2320]; Google;
   Omnibond and Science Gateways; Italian Ministry of Health;  {[}764/2021]},
Funding-Text = {We want to thank Matteo Ballabio for his contribution to the annotation
   process of data and to the preparation of the data publication. We thank
   Soichi Hayashi, the CTO of Brainlife, for his timely and invaluable
   support to publish data and code. C-MIND Acknowledgement Data used in
   the preparation of this article were obtained from the C-MIND Data
   Repository created by the C-MIND study of Normal Brain Development. This
   is a multisite, longitudinal study of typically developing children from
   ages newborn through young adulthood conducted by Cincinnati Children's
   Hospital Medical Center and UCLA and supported by the National Institute
   of Child Health and Human Development (Contract \#s HHSN275200900018C).
   A listing of the participating sites and a complete listing of the study
   investigators can be found at https://research.cchmc.org/c-mind.This
   manuscript reflects the views of the authors and may not reflect the
   opinions or views of the NIH. Pediatric MRI Acknowledgement Data used in
   the preparation of this article were obtained from the NIH Pediatric MRI
   Data Repository created by the NIH MRI Study of Normal Brain
   Development. This is a multisite, longitudinal study of typically
   developing children from ages newborn through young adulthood conducted
   by the Brain Development Cooperative Group and supported by the National
   Institute of Child Health and Human Development, the National Institute
   on Drug Abuse, the National Institute of Mental Health, and the National
   Institute of Neurological Disorders and Stroke (Contract \#s
   N01-HD02-3343, N01-MH90002, and N01-NS-9-2314, -2315, -2316, -2317,
   -2319 and -2320). This work was partially supported by the grant PAT
   Reg. n. 764/2021 NeuSurPlan. This work is partially funded by ``Machine
   Learning Research and Education on Neuroscience Data by connecting
   Google Cloud and brainlife.io{''}-Cloudify Gateways 2020, supported by
   Google, Omnibond and Science Gateways. This work was supported by the
   Italian Ministry of Health ({''}Ricerca Corrente{''} to Denis Peruzzo)
   and by ``5 per mille{''} funds for biomedical research.},
Number-of-Cited-References = {73},
Times-Cited = {5},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {4},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {4R9MQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000857079000007},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000711661600029,
Author = {Butt, Adeel A. and Yan, Peng and Shaikh, Obaid S. and Mayr, Florian B.},
Title = {Outcomes among patients with breakthrough SARS-CoV-2 infection after
   vaccination in a high-risk national population},
Journal = {ECLINICALMEDICINE},
Year = {2021},
Volume = {40},
Month = {OCT},
Abstract = {Background: Breakthrough infections after SARS-CoV-2 infection have been
   reported. Clinical outcomes among persons with breakthrough infection
   are not known. Methods: We retrospectively identified all Veterans with
   a confirmed SARS-CoV-2 infection >14 days after the second dose of
   either Pfizer-BNT-162b2 or Moderna-mRNA-1273 vaccine between December
   15, 2020 and March 30, 2021, and age, race, sex, body mass index,
   Charlson comorbidity index, geographical location, and date of positive
   test matched unvaccinated controls with SARS-CoV-2 infection. Our
   primary endpoint was the rate of severe disease or death defined as
   hospitalization, admission to ICU, mechanical ventilation, or death in
   both groups. Findings: Among 258,716 persons with both doses of vaccines
   and 756,150 without any vaccination, we identified 271 (0.1\%)
   vaccinated persons with breakthrough infection and 48,114 (6.4\%)
   unvaccinated matched controls with infection between December 15, 2020
   and March 30, 2021. Among 213 matched pairs, symptoms were present in
   33.3\% of those with breakthrough infection and 42.2\% of the controls.
   A total of 79 persons met the definition of severe disease or death (42
   in the breakthrough infection group and 37 in the control group). Rate
   of severe disease or death per 1,000 person-days (95\% CI) was 4.08
   (2.84,5.31) among those with breakthrough infection and 3.6 (2.53,4.73)
   among the controls (P = 0.58). Rate was similar among both groups
   regardless of age-group, race, BMI or presence of comorbidities. Among
   persons with breakthrough infection and matched controls with infection,
   vaccination was not associated with a lower risk of severe disease or
   death in the main analyses but was associated with a lower risk when
   matching did not include geographic location (HR 0.62, 95\% CI
   0.43,0.91). Interpretation: Demographic or clinical factors are not
   associated with a lower risk of severe disease or death in persons with
   breakthrough SARS-CoV-2 infection. Funding: None (c) 2021 The Authors.
   Published by Elsevier Ltd. This is an open access article under the CC
   BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Butt, AA (Corresponding Author), Weill Cornell Med Coll, New York, NY 10021 USA.
   Butt, AA (Corresponding Author), Weill Cornell Med Coll, Doha, Qatar.
   Butt, Adeel A.; Yan, Peng; Shaikh, Obaid S.; Mayr, Florian B., VA Pittsburgh Healthcare Syst, Pittsburgh, PA USA.
   Butt, Adeel A., Weill Cornell Med Coll, New York, NY 10021 USA.
   Butt, Adeel A., Weill Cornell Med Coll, Doha, Qatar.
   Butt, Adeel A., Hamad Med Corp, Doha, Qatar.
   Shaikh, Obaid S.; Mayr, Florian B., Univ Pittsburgh, Med Ctr, Pittsburgh, PA USA.},
DOI = {10.1016/j.eclinm.2021.101117},
EarlyAccessDate = {AUG 2021},
Article-Number = {101117},
EISSN = {2589-5370},
Keywords = {Sars-CoV-2; Vaccination; Outcomes; Breakthrough infection},
Research-Areas = {General \& Internal Medicine},
Web-of-Science-Categories  = {Medicine, General \& Internal},
Author-Email = {aab2005@qatar-med.cornell.edu},
Affiliations = {US Department of Veterans Affairs; Veterans Health Administration (VHA);
   VA Pittsburgh Healthcare System; Cornell University; Weill Cornell
   Medicine; Qatar Foundation (QF); Weill Cornell Medical College Qatar;
   Hamad Medical Corporation; Pennsylvania Commonwealth System of Higher
   Education (PCSHE); University of Pittsburgh},
ORCID-Numbers = {Butt, Adeel/0000-0002-1118-1826},
Funding-Acknowledgement = {Department of Veterans Affairs (VA) Informatics and Computing
   Infrastructure (VINCI) {[}VA HSR RES 13-457]},
Funding-Text = {This study was supported by data created by the VA COVID-19 Shared Data
   Resource and resources and facilities of the Department of Veterans
   Affairs (VA) Informatics and Computing Infrastructure (VINCI), VA HSR
   RES 13-457. This material is the result of work is also supported with
   resources and the use of facilities at the VA Pittsburgh Healthcare
   System and the central data repositories maintained by the VA
   Information Resource Center, including the Corporate Data Warehouse. The
   views expressed in this article are those of the authors and do not
   necessarily reflect the position or policy of the Department of Veterans
   Affairs or the funding agencies.},
Number-of-Cited-References = {16},
Times-Cited = {21},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {EClinicalMedicine},
Doc-Delivery-Number = {WN3GW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000711661600029},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000702325300001,
Author = {Zech, Michael and Kumar, Kishore R. and Reining, Sophie and Reunert,
   Janine and Tchan, Michel and Riley, Lisa G. and Drew, Alexander P. and
   Adam, Robert J. and Berutti, Riccardo and Biskup, Saskia and Derive,
   Nicolas and Bakhtiari, Somayeh and Jin, Sheng Chih and Kruer, Michael C.
   and Bardakjian, Tanya and Gonzalez-Alegre, Pedro and Sarmiento, Ignacio
   J. Keller and Mencacci, Niccolo E. and Lubbe, Steven J. and Kurian,
   Manju A. and Clot, Fabienne and Meneret, Aurelie and Agathe,
   Jean-Madeleine de Sainte and Fung, Victor S. C. and Vidailhet, Marie and
   Baumann, Matthias and Marquardt, Thorsten and Winkelmann, Juliane and
   Boesch, Sylvia},
Title = {Biallelic <i>AOPEP</i> Loss-of-Function Variants Cause Progressive
   Dystonia with Prominent Limb Involvement},
Journal = {MOVEMENT DISORDERS},
Year = {2022},
Volume = {37},
Number = {1},
Pages = {137-147},
Month = {JAN},
Abstract = {Background Monogenic causes of isolated dystonia are heterogeneous.
   Assembling cohorts of affected individuals sufficiently large to
   establish new gene-disease relationships can be challenging. Objective
   We sought to expand the catalogue of monogenic etiologies for isolated
   dystonia. Methods After the discovery of a candidate variant in a
   multicenter exome-sequenced cohort of affected individuals with
   dystonia, we queried online platforms and genomic data repositories
   worldwide to identify subjects with matching genotypic profiles. Results
   Seven different biallelic loss-of-function variants in AOPEP were
   detected in five probands from four unrelated families with strongly
   overlapping phenotypes. In one proband, we observed a homozygous
   nonsense variant (c.1477C>T {[}p.Arg493{*}]). A second proband harbored
   compound heterozygous nonsense variants (c.763C>T {[}p.Arg255{*}];
   c.777G>A {[}p.Trp259{*}]), whereas a third proband possessed a
   frameshift variant (c.696\_697delAG {[}p.Ala234Serfs{*}5]) in trans with
   a splice-disrupting alteration (c.2041-1G>A). Two probands (siblings)
   from a fourth family shared compound heterozygous frameshift alleles
   (c.1215delT {[}p.Val406Cysfs{*}14]; c.1744delA {[}p.Met582Cysfs{*}6]).
   All variants were rare and expected to result in truncated proteins
   devoid of functionally important amino acid sequence. AOPEP, widely
   expressed in developing and adult human brain, encodes a zinc-dependent
   aminopeptidase, a member of a class of proteolytic enzymes implicated in
   synaptogenesis and neural maintenance. The probands presented with
   disabling progressive dystonia predominantly affecting upper and lower
   extremities, with variable involvement of craniocervical muscles.
   Dystonia was unaccompanied by any additional symptoms in three families,
   whereas the fourth family presented co-occurring late-onset
   parkinsonism. Conclusions Our findings suggest a likely causative role
   of predicted inactivating biallelic AOPEP variants in cases of autosomal
   recessive dystonia. Additional studies are warranted to understand the
   pathophysiology associated with loss-of-function variation in AOPEP. (c)
   2021 The Authors. Movement Disorders published by Wiley Periodicals LLC
   on behalf of International Parkinson and Movement Disorder Society},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Zech, M (Corresponding Author), Deutsch Forschungszentrum Gesundheit \& Umwelt Gmb, Helmholtz Zentrum Munchen, Inst Neurogen, Ingolstadter Landstr 1, D-85764 Neuherberg, Germany.
   Zech, Michael; Berutti, Riccardo; Winkelmann, Juliane, Helmholtz Zentrum Munchen, Inst Neurogen, Munich, Germany.
   Zech, Michael; Berutti, Riccardo; Winkelmann, Juliane, Tech Univ Munich, Munich, Germany.
   Zech, Michael; Berutti, Riccardo; Winkelmann, Juliane, Tech Univ Munich, Sch Med, Inst Human Genet, Munich, Germany.
   Kumar, Kishore R., Univ Sydney, Concord Repatriat Gen Hosp, Concord Clin Sch, Mol Med Lab \& Neurol Dept, Sydney, NSW, Australia.
   Kumar, Kishore R.; Drew, Alexander P., Garvan Inst Med Res, Kinghorn Ctr Clin Genom, Darlinghurst, NSW, Australia.
   Reining, Sophie; Reunert, Janine; Marquardt, Thorsten, Univ Munster, Dept Gen Paediat, Munster, Germany.
   Tchan, Michel, Westmead Hosp, Dept Genet Med, Westmead, NSW, Australia.
   Tchan, Michel, Univ Sydney, Sydney Med Sch, Camperdown, NSW, Australia.
   Riley, Lisa G., Univ Sydney, Sydney Med Sch, Discipline Child \& Adolescent Hlth, Sydney, NSW, Australia.
   Riley, Lisa G., Childrens Hosp Westmead, Kids Res, Rare Dis Funct Genom, Sydney, NSW, Australia.
   Riley, Lisa G., Childrens Med Res Inst, Sydney, NSW, Australia.
   Adam, Robert J., Royal Brisbane \& Womens Hosp, Dept Neurol, Brisbane, Qld, Australia.
   Adam, Robert J., Univ Queensland, Ctr Clin Res, Brisbane, Qld, Australia.
   Biskup, Saskia, CeGaT GmbH, Tubingen, Germany.
   Biskup, Saskia, Praxis Humangenet Tubingen, Tubingen, Germany.
   Derive, Nicolas; Clot, Fabienne; Agathe, Jean-Madeleine de Sainte, Lab Biol Med Multisites SeqOIA, Paris, France.
   Bakhtiari, Somayeh; Kruer, Michael C., Phoenix Childrens Hosp, Barrow Neurol Inst, Div Pediat Neurol, Pediat Movement Disorders Program, Phoenix, AZ USA.
   Bakhtiari, Somayeh; Kruer, Michael C., Univ Arizona, Arizona Coll Med, Dept Child Hlth, Phoenix, AZ USA.
   Bakhtiari, Somayeh; Kruer, Michael C., Univ Arizona, Arizona Coll Med, Dept Cellular, Phoenix, AZ USA.
   Bakhtiari, Somayeh; Kruer, Michael C., Univ Arizona, Arizona Coll Med, Dept Mol Med, Phoenix, AZ USA.
   Bakhtiari, Somayeh; Kruer, Michael C., Univ Arizona, Arizona Coll Med, Program Genet, Phoenix, AZ USA.
   Jin, Sheng Chih, Washington Univ, Sch Med, Dept Genet, St Louis, MO 63110 USA.
   Bardakjian, Tanya; Gonzalez-Alegre, Pedro, Univ Penn, Perelman Sch Med, Dept Neurol, Philadelphia, PA 19104 USA.
   Sarmiento, Ignacio J. Keller; Mencacci, Niccolo E.; Lubbe, Steven J., Northwestern Univ, Feinberg Sch Med, Ken \& Ruth Davee Dept Neurol, Chicago, IL 60611 USA.
   Sarmiento, Ignacio J. Keller; Mencacci, Niccolo E.; Lubbe, Steven J., Northwestern Univ, Feinberg Sch Med, Simpson Querrey Ctr Neurogenet, Chicago, IL 60611 USA.
   Kurian, Manju A., UCL Great Ormond St Inst Child Hlth, Dept Dev Neurosci, London, England.
   Kurian, Manju A., Great Ormond St Hosp Sick Children, Dept Neurol, London, England.
   Clot, Fabienne, Sorbonne Univ, Hop Pitie Salpetriere, AP HP, Dept Genet,UF Neurogenet Mol \& Cellulaire, Paris, France.
   Meneret, Aurelie; Vidailhet, Marie, Sorbonne Univ, Hop Pitie Salpetriere, AP HP, Paris Brain Inst,ICM,Inserm,CNRS,DMU Neurosci, Paris, France.
   Agathe, Jean-Madeleine de Sainte, Sorbonne Univ, Hop Pitie Salpetriere, AP HP, Lab Med Genom, Paris, France.
   Fung, Victor S. C., Westmead Hosp, Neurol Dept, Movement Disorders Unit, Westmead, NSW, Australia.
   Fung, Victor S. C., Univ Sydney, Sydney Med Sch, Sydney, NSW, Australia.
   Baumann, Matthias, Med Univ Innsbruck, Dept Pediat, Innsbruck, Austria.
   Winkelmann, Juliane, Tech Univ Munich, Lehrstuhl Neurogenet, Munich, Germany.
   Winkelmann, Juliane, SyNergy, Munich Cluster Syst Neurol, Munich, Germany.
   Boesch, Sylvia, Med Univ Innsbruck, Dept Neurol, Innsbruck, Austria.},
DOI = {10.1002/mds.28804},
EarlyAccessDate = {OCT 2021},
ISSN = {0885-3185},
EISSN = {1531-8257},
Keywords = {AOPEP; monogenic dystonia; genomic analysis; loss-of-function variants;
   rare disease},
Keywords-Plus = {AMINOPEPTIDASE},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Clinical Neurology},
Author-Email = {michael.zech@mri.tum.de},
Affiliations = {Helmholtz Association; Helmholtz-Center Munich - German Research Center
   for Environmental Health; Technical University of Munich; Technical
   University of Munich; University of Sydney; Concord Repatriation General
   Hospital; Garvan Institute of Medical Research; University of Munster;
   NSW Health; Westmead Hospital; University of Sydney; University of
   Sydney; University of Sydney; University of Sydney; NSW Health; The
   Children's Hospital at Westmead; Children's Medical Research Institute -
   Australia; University of Sydney; Royal Brisbane \& Women's Hospital;
   University of Queensland; CeGaT; CeGaT; Barrow Neurological Institute;
   Phoenix Children's Hospital; University of Arizona; University of
   Arizona; University of Arizona; University of Arizona; Washington
   University (WUSTL); University of Pennsylvania; Northwestern University;
   Feinberg School of Medicine; Northwestern University; Feinberg School of
   Medicine; University of London; University College London; University of
   London; University College London; Great Ormond Street Hospital for
   Children NHS Foundation Trust; Assistance Publique Hopitaux Paris
   (APHP); Hopital Universitaire Paul-Brousse - APHP; Sorbonne Universite;
   Universite Paris Cite; Hopital Universitaire Hotel-Dieu - APHP; Hopital
   Universitaire Pitie-Salpetriere - APHP; Institut National de la Sante et
   de la Recherche Medicale (Inserm); Assistance Publique Hopitaux Paris
   (APHP); Hopital Universitaire Pitie-Salpetriere - APHP; Centre National
   de la Recherche Scientifique (CNRS); Universite Paris Cite; Hopital
   Universitaire Hotel-Dieu - APHP; Sorbonne Universite; Hopital
   Universitaire Paul-Brousse - APHP; Assistance Publique Hopitaux Paris
   (APHP); Hopital Universitaire Paul-Brousse - APHP; Sorbonne Universite;
   Universite Paris Cite; Hopital Universitaire Hotel-Dieu - APHP; Hopital
   Universitaire Pitie-Salpetriere - APHP; NSW Health; Westmead Hospital;
   University of Sydney; University of Sydney; Medical University of
   Innsbruck; Technical University of Munich; Medical University of
   Innsbruck},
ResearcherID-Numbers = {Fung, Victor SC/AGK-1296-2022
   Adam, Robert/J-5318-2013
   },
ORCID-Numbers = {Fung, Victor SC/0000-0003-3085-2282
   Adam, Robert/0000-0003-0053-7919
   Boesch, Sylvia/0000-0003-1657-7368
   Drew, Alexander/0000-0001-5701-0654
   Jin, Sheng Chih/0000-0002-5777-7262
   de Sainte Agathe, Jean-Madeleine/0000-0002-7753-8226},
Funding-Acknowledgement = {Technische Universitat Munchen (Munich, Germany); Helmholtz Zentrum
   Munchen (Munich, Germany); Medizinische Universitat Innsbruck
   (Innsbruck, Austria); German Research Foundation (DFG) {[}DFG 458949627,
   ZE 1213/2-1, WI 1820/14-1]; European Reference Network for Rare
   Neurological Diseases {[}739510]; Paul Ainsworth Family Foundation;
   Projekt DEAL},
Funding-Text = {This study was funded by in-house institutional funding from Technische
   Universitat Munchen (Munich, Germany), Helmholtz Zentrum Munchen
   (Munich, Germany), and Medizinische Universitat Innsbruck (Innsbruck,
   Austria). M.Z. and J.W. received research support from the German
   Research Foundation (DFG 458949627, ZE 1213/2-1, and WI 1820/14-1). S.
   Boesch is a member of the European Reference Network for Rare
   Neurological Diseases (Project ID No. 739510). K.R.K. received funding
   from the Paul Ainsworth Family Foundation. We thank the families who
   participated in this study. We thank Dora Steel, BMBCh (Great Ormond
   Street Hospital, London, UK) for querying genomic data for AOPEP
   variants. Biospecimens used in the analyses presented in this article
   were obtained from the Northwestern University Movement Disorders Center
   (MDC) Biorepository. As such, the investigators within MDC Biorepository
   contributed to the design and implementation of the MDC Biorepository
   and/or provided data and collected biospecimens but did not participate
   in the analysis or writing of this report. MDC Biorepository
   investigators include: Tanya Simuni, MD; Dimitri Krainc, MD, PhD; Opal
   Puneet, MD, PhD; Cindy Zadikoff, MD; Onur Melen, MD; Danny Bega, MD;
   Roneil G. Malkani, MD; Steven Lubbe, PhD; Niccolo E. Mencacci, MD, PhD;
   Christina Zelano, PhD; Joanna Blackburn, MD; Firas Wehbe, MD, PhD; Lisa
   Kinsley, MS, CGC; and Tina Ward, MS. A gift from the Malkin family
   generously supported the work of the MDC Biorepository. We gratefully
   thank Laurene Tissier, MLT, for her generous contribution with Sanger
   sequencing of individuals from family IV. Open Access funding enabled
   and organized by Projekt DEAL.},
Number-of-Cited-References = {35},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Mov. Disord.},
Doc-Delivery-Number = {YW6SP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000702325300001},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000417973300064,
Author = {Phillips, Mason and Fomel, Sergey},
Title = {Plane-wave Sobel attribute for discontinuity enhancement in seismic
   images},
Journal = {GEOPHYSICS},
Year = {2017},
Volume = {82},
Number = {6},
Pages = {WB63-WB69},
Month = {NOV-DEC},
Abstract = {Discontinuity enhancement attributes are commonly used to facilitate the
   interpretation process by enhancing edges in seismic images and
   providing a quantitative measure of the significance of discontinuous
   features. These attributes require careful preprocessing to maintain
   geologic features and suppress acquisition and processing artifacts,
   which may be artificially detected as a geologic edge. We have developed
   the plane-wave Sobel attribute, a modification of the classic Sobel
   filter, by orienting the filter along seismic structures using
   plane-wave destruction and plane-wave shaping. The plane-wave Sobel
   attribute can be applied directly to a seismic image to efficiently and
   effectively enhance discontinuous features or to a coherence image to
   create a sharper and more detailed image. Two field benchmark data
   examples with many faults and channel features from offshore New Zealand
   and offshore Nova Scotia demonstrate the effectiveness of this method
   compared with conventional coherence attributes. The results are
   reproducible using the Madagascar software package.},
Publisher = {SOC EXPLORATION GEOPHYSICISTS - SEG},
Address = {8801 S YALE ST, TULSA, OK 74137 USA},
Type = {Article},
Language = {English},
Affiliation = {Phillips, M (Corresponding Author), Univ Texas Austin, John A \& Katherine G Jackson Sch Geosci, Bur Econ Geol, Austin, TX 78712 USA.
   Phillips, Mason; Fomel, Sergey, Univ Texas Austin, John A \& Katherine G Jackson Sch Geosci, Bur Econ Geol, Austin, TX 78712 USA.},
DOI = {10.1190/GEO2017-0233.1},
ISSN = {0016-8033},
EISSN = {1942-2156},
Keywords-Plus = {FAULT SURFACES; COHERENCE},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {mdp2383@utexas.edu
   sergey.fomel@beg.utexas.edu},
Affiliations = {University of Texas System; University of Texas Austin},
ResearcherID-Numbers = {Phillips, Mason/AAV-4362-2021
   Fomel, Sergey B/A-3100-2009
   },
ORCID-Numbers = {Fomel, Sergey B/0000-0002-9024-5137
   Phillips, Mason/0000-0003-0191-5774},
Funding-Acknowledgement = {Texas Consortium for Computational Seismology},
Funding-Text = {We thank the Nova Scotia Department of Energy, Canada-Nova Scotia
   Offshore Petroleum Board, and New Zealand Petroleum and Minerals for
   providing data used in this paper to the SEG open data repository. We
   thank the sponsors of the Texas Consortium for Computational Seismology
   for financial support. We thank X. Wu and R. Swindeman for helpful
   comments and discussions. The computational examples reported in this
   paper are reproducible using the Madagascar open-source software package
   (Fomel et al., 2013).},
Number-of-Cited-References = {35},
Times-Cited = {11},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Geophysics},
Doc-Delivery-Number = {FP9MR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000417973300064},
DA = {2024-01-15},
}

@article{ WOS:000459839000020,
Author = {Drewitt, James W. E. and Walter, Michael J. and Zhang, Hongluo and
   McMahon, Sorcha C. and Edwards, David and Heinen, Benedict J. and Lord,
   Oliver T. and Anzellini, Simone and Kleppe, Annette K.},
Title = {The fate of carbonate in oceanic crust subducted into earth's lower
   mantle},
Journal = {EARTH AND PLANETARY SCIENCE LETTERS},
Year = {2019},
Volume = {511},
Pages = {213-222},
Month = {APR 1},
Abstract = {We report on laser-heated diamond anvil cell (LHDAC) experiments in the
   FeO-MgO-SiO2-CO2 (FMSC) and CaO-MgO-SiO2-CO2 (CMSC) systems at lower
   mantle pressures designed to test for decarbonation and diamond forming
   reactions. Sub-solidus phase relations based on synthesis experiments
   are reported in the pressure range of similar to 35 to 90 GPa at
   temperatures of similar to 1600 to 2200 K. Ternary bulk compositions
   comprised of mixtures of carbonate and silica are constructed such that
   decarbonation reactions produce non-ternary phases (e.g. bridgmanite,
   Ca-perovskite, diamond, CO2-V), and synchrotron X-ray diffraction and
   micro-Raman spectroscopy are used to identify the appearance of reaction
   products. We find that carbonate phases in these two systems react with
   silica to form bridgmanite +/- Ca-perovskite + CO2 at pressures in the
   range of similar to 40 to 70 GPa and 1600 to 1900 K in decarbonation
   reactions with negative Clapeyron slopes. Our results show that
   decarbonation reactions form an impenetrable barrier to subduction of
   carbonate in oceanic crust to depths in the mantle greater than similar
   to 1500 km. We also identify carbonate and CO2-V dissociation reactions
   that form diamond plus oxygen. On the basis of the observed
   decarbonation reactions we predict that the ultimate fate of carbonate
   in oceanic crust subducted into the deep lower mantle is in the form of
   refractory diamond in the deepest lower mantle along a slab geotherm and
   throughout the lower mantle along a mantle geotherm. Diamond produced in
   oceanic crust by subsolidus decarbonation is refractory and immobile and
   can be stored at the base of the mantle over long timescales,
   potentially returning to the surface in OIB magmas associated with deep
   mantle plumes. (C) 2019 The Authors. Published by Elsevier B.V. This is
   an open access article under the CC BY license.},
Publisher = {ELSEVIER SCIENCE BV},
Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Walter, MJ (Corresponding Author), Univ Bristol, Sch Earth Sci, Wills Mem Bldg,Queens Rd, Bristol BS8 1RJ, Avon, England.
   Walter, MJ (Corresponding Author), Carnegie Inst Sci, Geophys Lab, 5251 Broad Branch Rd NW, Washington, DC 20015 USA.
   Drewitt, James W. E.; Walter, Michael J.; Zhang, Hongluo; McMahon, Sorcha C.; Edwards, David; Heinen, Benedict J.; Lord, Oliver T., Univ Bristol, Sch Earth Sci, Wills Mem Bldg,Queens Rd, Bristol BS8 1RJ, Avon, England.
   Walter, Michael J., Carnegie Inst Sci, Geophys Lab, 5251 Broad Branch Rd NW, Washington, DC 20015 USA.
   Zhang, Hongluo, Univ Sci \& Technol China, Sch Earth \& Space Sci, 96 Jinzhai RD, Hefei 230026, Anhui, Peoples R China.
   Anzellini, Simone; Kleppe, Annette K., Diamond Light Source Ltd, Diamond House,Harwell Sci \& Innovat Campus, Chilton OX11 0DE, England.},
DOI = {10.1016/j.epsl.2019.01.041},
ISSN = {0012-821X},
EISSN = {1385-013X},
Keywords = {carbonate; subduction; lower mantle; decarbonation; diamond},
Keywords-Plus = {HIGH-PRESSURE; HIGH-TEMPERATURE; MELTING CURVE; DIAMOND; STABILITY;
   MAGNESITE; DOLOMITE; ECLOGITE; PHASE; CACO3},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {mwalter@carnegiescience.edu},
Affiliations = {University of Bristol; Carnegie Institution for Science; Chinese Academy
   of Sciences; University of Science \& Technology of China, CAS; Diamond
   Light Source},
ResearcherID-Numbers = {Drewitt, James W E/A-1631-2010
   Lord, Oliver T/D-4663-2014
   Anzellini, Simone/O-7404-2019
   },
ORCID-Numbers = {Drewitt, James W E/0000-0002-3510-4155
   Lord, Oliver T/0000-0003-0563-1293
   Anzellini, Simone/0000-0003-0091-3902
   Zhang, Hongluo/0000-0001-7604-4876
   Heinen, Benedict J/0000-0003-3562-7439},
Funding-Acknowledgement = {NERC {[}NE/M000419/1, NE/J018945/1]; Royal Society {[}UF150057]; NERC
   {[}NE/J018945/1, NE/P002951/1, NE/M000117/1, NE/M000419/1] Funding
   Source: UKRI},
Funding-Text = {Financial support for this study was provided by NERC grant NE/M000419/1
   to M.J. Walter. O.T. Lord would like to acknowledge support from the
   Royal Society in the form of a University Research Fellowship (UF150057)
   and from the NERC in the form of a post-doctoral research fellowship
   (NE/J018945/1). We acknowledge the ESRF for provision of beam time under
   proposal ES736 and G. Garborino for their assistance at beamline ID27.
   We thank A. Thomson, C. Gregson, M. Baron, and D. Daisenberger, for
   their assistance during synchrotron beamtime at the DLS. Measurements at
   DLS were made under beamtime awards EE10617, EE11896, EE15288, and
   EE17994. Data are available at the University of Bristol data
   repository, data.bris, at
   https://doLorg/10.5523/bris.75f6kxwjf3m02cc74duvve592.},
Number-of-Cited-References = {71},
Times-Cited = {22},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {44},
Journal-ISO = {Earth Planet. Sci. Lett.},
Doc-Delivery-Number = {HM9XT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000459839000020},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000483167600001,
Author = {Sullivan, Alexander and Purohit, Priyank K. and Freese, Nowlan H. and
   Pasha, Asher and Esteban, Eddi and Waese, Jamie and Wu, Alison and Chen,
   Michelle and Chin, Chih Y. and Song, Richard and Watharkar, Sneha R. and
   Chan, Agnes P. and Krishnakumar, Vivek and Vaughn, Matthew W. and Town,
   Chris and Loraine, Ann E. and Provart, Nicholas J.},
Title = {An `eFP-Seq Browser' for visualizing and exploring RNA sequencing data},
Journal = {PLANT JOURNAL},
Year = {2019},
Volume = {100},
Number = {3},
Pages = {641-654},
Month = {NOV},
Abstract = {Improvements in next-generation sequencing technologies have resulted in
   dramatically reduced sequencing costs. This has led to an explosion of
   `-seq'-based methods, of which RNA sequencing (RNA-seq) for generating
   transcriptomic data is the most popular. By analysing global patterns of
   gene expression in organs/tissues/cells of interest or in response to
   chemical or environmental perturbations, researchers can better
   understand an organism's biology. Tools designed to work with large
   RNA-seq data sets enable analyses and visualizations to help generate
   hypotheses about a gene's function. We present here a user-friendly
   RNA-seq data exploration tool, called the `eFP-Seq Browser', that shows
   the read map coverage of a gene of interest in each of the samples along
   with `electronic fluorescent pictographic' (eFP) images that serve as
   visual representations of expression levels. The tool also summarizes
   the details of each RNA-seq experiment, providing links to archival
   databases and publications. It automatically computes the reads per
   kilobase per million reads mapped expression-level summaries and point
   biserial correlation scores to sort the samples based on a gene's
   expression level or by how dissimilar the read map profile is from a
   gene splice variant, to quickly identify samples with the strongest
   expression level or where alternative splicing might be occurring. Links
   to the Integrated Genome Browser desktop visualization tool allow
   researchers to visualize and explore the details of RNA-seq alignments
   summarized in eFP-Seq Browser as coverage graphs. We present four cases
   of use of the eFP-Seq Browser for ABI3, SR34, SR45a and U2AF65B, where
   we examine expression levels and identify alternative splicing. The URL
   for the browser is . Open research badges This article has earned an
   Open Data Badge for making publicly available the digitally-shareable
   data necessary to reproduce the reported results. Tool is at ; RNA-seq
   data at and . Code is available at},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Provart, NJ (Corresponding Author), Univ Toronto, CAGEF, Dept Cell \& Syst Biol, Toronto, ON, Canada.
   Loraine, AE (Corresponding Author), Univ North Carolina Charlotte, Charlotte, NC 28223 USA.
   Sullivan, Alexander; Purohit, Priyank K.; Pasha, Asher; Esteban, Eddi; Waese, Jamie; Wu, Alison; Chen, Michelle; Chin, Chih Y.; Song, Richard; Provart, Nicholas J., Univ Toronto, CAGEF, Dept Cell \& Syst Biol, Toronto, ON, Canada.
   Freese, Nowlan H.; Watharkar, Sneha R.; Loraine, Ann E., Univ North Carolina Charlotte, Charlotte, NC 28223 USA.
   Chan, Agnes P.; Krishnakumar, Vivek; Town, Chris, J Craig Venter Inst, Rockville, MD USA.
   Vaughn, Matthew W., Univ Texas Austin, Texas Adv Comp Ctr, Austin, TX 78712 USA.},
DOI = {10.1111/tpj.14468},
EarlyAccessDate = {AUG 2019},
ISSN = {0960-7412},
EISSN = {1365-313X},
Keywords = {Arabidopsis thaliana; data visualization; plant growth; RNA processing;
   RNA-seq; temperature stress},
Keywords-Plus = {INTEGRATED GENOME BROWSER; READ ALIGNMENT; ARABIDOPSIS; ANNOTATION},
Research-Areas = {Plant Sciences},
Web-of-Science-Categories  = {Plant Sciences},
Author-Email = {ann.loraine@uncc.edu
   nicholas.provart@utoronto.ca},
Affiliations = {University of Toronto; University of North Carolina; University of North
   Carolina Charlotte; J. Craig Venter Institute; University of Texas
   System; University of Texas Austin},
ResearcherID-Numbers = {Krishnakumar, Vivek/C-7204-2015
   Wilson, Matthew H/K-3193-2013
   },
ORCID-Numbers = {Krishnakumar, Vivek/0000-0002-5227-0200
   Vaughn, Matthew/0000-0002-1384-4283
   Loraine, Ann/0000-0002-8365-0177
   Sullivan, Alexander/0000-0002-4463-4473
   Pasha, Asher/0000-0002-9315-0520},
Funding-Acknowledgement = {Genome Canada/Ontario Genomics grant {[}5452]; National Institutes of
   Health {[}R01-GM1034 63]},
Funding-Text = {We are thankful to Nirav Merchant for suggesting that we custom compile
   SAMTOOLS to access BAM files in Amazon's S3 storage. This work was
   funded by Genome Canada/Ontario Genomics grant 5452, `Large Data Sets
   and Novel Tools for Plant Biology for use in International
   Consolidation-Tier Data Repositories and Portals'. National Institutes
   of Health, R01-GM1034 63.},
Number-of-Cited-References = {29},
Times-Cited = {22},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {13},
Journal-ISO = {Plant J.},
Doc-Delivery-Number = {JR9GL},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000483167600001},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000701820800001,
Author = {Schoger, Eric and Zimmermann, Wolfram-Hubertus and Cyganek, Lukas and
   Zelarayan, Laura Cecilia},
Title = {Establishment of a second generation homozygous CRISPRa human induced
   pluripotent stem cell (hiPSC) line for enhanced levels of endogenous
   gene activation},
Journal = {STEM CELL RESEARCH},
Year = {2021},
Volume = {56},
Month = {OCT},
Abstract = {CRISPR/Cas9 technology based on nuclease inactive dCas9 and fused to the
   heterotrimeric VPR transcriptional activator is a powerful tool to
   enhance endogenous transcription by targeting defined genomic loci. We
   generated homozygous human induced pluripotent stem cell (hiPSC) lines
   carrying dCas9 fused to VPR along with a WPRE element at the AAVS1 locus
   (CRISPRa2). We demonstrated pluripotency, genomic integrity and
   differentiation potential into all three germ layers. CRISPRa2 cells
   showed increased transgene expression and higher transcriptional
   induction in hiPSC-derived cardiomyocytes compared to a previously
   described CRISPRa line. Both lines allow studying endogenous
   transcriptional modulation with lower and higher transcript abundance.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Schoger, E; Zelarayán, LC (Corresponding Author), Univ Med Ctr Goettingen UMG, Inst Pharmacol \& Toxicol, Gottingen, Germany.
   Schoger, E; Zelarayán, LC (Corresponding Author), DZHK German Ctr Cardiovasc Res, Partner Site Gottingen, Gottingen, Germany.
   Schoger, Eric; Zimmermann, Wolfram-Hubertus; Zelarayan, Laura Cecilia, Univ Med Ctr Goettingen UMG, Inst Pharmacol \& Toxicol, Gottingen, Germany.
   Schoger, Eric; Zimmermann, Wolfram-Hubertus; Cyganek, Lukas; Zelarayan, Laura Cecilia, DZHK German Ctr Cardiovasc Res, Partner Site Gottingen, Gottingen, Germany.
   Zimmermann, Wolfram-Hubertus, Univ Gottingen, Cluster Excellence Multiscale Bioimaging Mol Mach, Gottingen, Germany.
   Zimmermann, Wolfram-Hubertus, DZNE German Ctr Neurodegenerat Dis, Partner Site Gottingen, Gottingen, Germany.
   Zimmermann, Wolfram-Hubertus, Fraunhofer Inst Translat Med \& Pharmacol ITMP, Gottingen, Germany.
   Cyganek, Lukas, Univ Med Ctr Gottingen UMG, Clin Cardiol \& Pneumol, Gottingen, Germany.},
DOI = {10.1016/j.scr.2021.102518},
EarlyAccessDate = {SEP 2021},
Article-Number = {102518},
ISSN = {1873-5061},
EISSN = {1876-7753},
Research-Areas = {Cell Biology; Biotechnology \& Applied Microbiology},
Web-of-Science-Categories  = {Cell \& Tissue Engineering; Biotechnology \& Applied Microbiology; Cell
   Biology},
Author-Email = {eric.schoger@med.uni-goettingen.de
   laura.zelarayan@med.uni-goettingen.de},
Affiliations = {German Centre for Cardiovascular Research; University of Gottingen;
   Helmholtz Association; German Center for Neurodegenerative Diseases
   (DZNE)},
ResearcherID-Numbers = {Zelarayan, Laura C./Y-3715-2019
   },
ORCID-Numbers = {Zelarayan, Laura C./0000-0002-9001-0346
   Schoger, Eric/0000-0002-5485-9828
   Cyganek, Lukas/0000-0001-9120-1382},
Funding-Acknowledgement = {NIH Common Fund Regenerative Medicine Program {[}TC1133, RUCDRi002-A];
   NIH Common Fund; National Institute of Neurological Disorders and Stroke
   (NINDS) Human Cell and Data Repository (NHCDR) {[}50-001-21]; Open
   Access Publication Funds of the Gottingen University; DFG {[}SFB1002
   C07]; DZHK (German Center for Cardiovascular Research); Foundation
   Leducq},
Funding-Text = {Generation of the GMP line LhiPSC-GR1.1 (TC1133 or RUCDRi002-A) was
   supported by the NIH Common Fund Regenerative Medicine Program, and
   reported in Stem Cell Reports (Baghbaderani et al. 2015, doi:
   10.1016/j.stemcr.2015.08.015). The NIH Common Fund and the National
   Center for Advancing Translational Sciences (NCATS) are joint stewards
   of the LhiPSC-GR1.1 resource. The TC1133 line (Master Cell Bank Lot\#:
   50-001-21) was acquired by Repairon GmbH from the National Institute of
   Neurological Disorders and Stroke (NINDS) Human Cell and Data Repository
   (NHCDR) and processed to a GMP working cell bank (WCB). Post production
   cells from the WBC were kindly provided by Repairon to UMG for research
   use. We thank Yvonne Hintz, Kerstin Wenzel (Clinic for Cardiology and
   Pneumology, UMG), and Christina Weber (Institute of Pharmacology and
   Toxicology, UMG) for superb technical support. We acknowledge support by
   the Open Access Publication Funds of the Gottingen University. This work
   was supported by the DFG grant SFB1002 C07 and INF to LCZ; C04 to WHZ,
   S01 to LC/WHZ, the DZHK (German Center for Cardiovascular Research), and
   the Foundation Leducq.},
Number-of-Cited-References = {5},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Stem Cell Res.},
Doc-Delivery-Number = {UY9FK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000701820800001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000804688300016,
Author = {Rapuano, Kristina M. and Berrian, Nia and Baskin-Sommers, Arielle and
   Decarie-Spain, Lea and Sharma, Sandeep and Fulton, Stephanie and Casey,
   B. J. and Watts, Richard},
Title = {Longitudinal Evidence of a Vicious Cycle Between Nucleus Accumbens
   Microstructure and Childhood Weight Gain},
Journal = {JOURNAL OF ADOLESCENT HEALTH},
Year = {2022},
Volume = {70},
Number = {6},
Pages = {961-969},
Month = {JUN},
Abstract = {Purpose: Pediatric obesity is a growing public health concern. Previous
   work has observed diet to impact nucleus accumbens (NAcc) inflammation
   in rodents, measured by the reactive proliferation of glial cells.
   Recent work in humans has demonstrated a relationship between NAcc cell
   density a proxy for neuroinflammation-and weight gain in youth; however,
   the directionality of this relationship in the developing brain and
   association with diet remains unknown. Methods: Waist circumference (WC)
   and NAcc cell density were collected in a large cohort of children (n >
   2,000) participating in the Adolescent Brain Cognitive Development
   (ABCD) Study (release 3.0) at baseline (9-10 y) and at a Year 2
   follow-up (11-12 y). Latent change score modeling (LCSM) was used to
   disentangle contributions of baseline measures to two-year changes in WC
   percentile and NAcc cellularity. In addition, the role of NAcc
   cellularity in mediating the relationship between diet and WC percentile
   was assessed using dietary intake data collected at Year 2. Results:
   LCSM indicates that baseline WC percentile influences change in NAcc
   cellularity and that baseline NAcc cell density influences change in WC
   percentile. NAcc cellularity was significantly associated with WC
   percentile at Year 2 and mediated the relationship between dietary fat
   consumption and WC percentile. Conclusions: These results implicate a
   vicious cycle whereby NAcc cell density biases longitudinal changes in
   WC percentile and vice versa. Moreover, NAcc cell density may mediate
   the relationship between diet and weight gain in youth. These findings
   suggest that diet-induced inflammation of reward circuitry may lead to
   behavioral changes that further contribute to weight gain. (c) 2022
   Society for Adolescent Health and Medicine. Published by Elsevier Inc.
   This is an open access article under the CC BY license
   (http://creativecommons.org/licenses/by/4.0/).},
Publisher = {ELSEVIER SCIENCE INC},
Address = {STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA},
Type = {Article},
Language = {English},
Affiliation = {Rapuano, KM (Corresponding Author), Yale Univ, Dept Psychol, 2 Hillhouse Ave, New Haven, CT 06511 USA.
   Rapuano, Kristina M.; Berrian, Nia; Baskin-Sommers, Arielle; Casey, B. J.; Watts, Richard, Yale Univ, Dept Psychol, New Haven, CT 06520 USA.
   Decarie-Spain, Lea, Univ Southern Calif, Dept Biol Sci, Los Angeles 90007, CA USA.
   Sharma, Sandeep, Univ Calgary, Dept Comparat Biol \& Expt Med, Calgary, AB, Canada.
   Fulton, Stephanie, Univ Montreal \& Ctr Rech CHUM, Dept Nutr, Montreal, PQ, Canada.
   Rapuano, Kristina M., Yale Univ, Dept Psychol, 2 Hillhouse Ave, New Haven, CT 06511 USA.},
DOI = {10.1016/j.jadohealth.2022.01.002},
EarlyAccessDate = {MAY 2022},
ISSN = {1054-139X},
EISSN = {1879-1972},
Keywords = {Adolescent health; Pediatric obesity; Diet; Neuroinflammation; Nucleus
   accumbens; Restriction spectrum imaging},
Keywords-Plus = {BODY-MASS INDEX; WAIST-CIRCUMFERENCE; INDIVIDUAL-DIFFERENCES; FOOD
   COMMERCIALS; OBESITY; REWARD; INFLAMMATION; RATIO; OVERWEIGHT; ADIPOSITY},
Research-Areas = {Psychology; Public, Environmental \& Occupational Health; Pediatrics},
Web-of-Science-Categories  = {Psychology, Developmental; Public, Environmental \& Occupational Health;
   Pediatrics},
Author-Email = {kristina.rapuano@yale.edu},
Affiliations = {Yale University; University of Southern California; University of
   Calgary; Yale University},
ResearcherID-Numbers = {Watts, Richard/AEU-2679-2022
   },
ORCID-Numbers = {Watts, Richard/0000-0003-1026-2293
   Baskin-Sommers, Arielle/0000-0001-6773-0508
   Casey, BJ/0000-0003-2905-9834},
Funding-Acknowledgement = {NIH;  {[}U01 DA041174];  {[}R01DK097399-01]},
Funding-Text = {The ABCD Study is supported by the NIH and additional fed-U24DA041123,
   and U24DA041147. A full list of supporters is available at
   https://abcdstudy.org/federal-partners.html. A listing of participating
   sites and a complete listing of the study investigators can be found at
   https://abcdstudy.org/consortium\_ members/. ABCD consortium
   investigators designed and implemented the study and/or provided data
   but did not necessarily participate in the analysis or writing of this
   report. This manuscript reflects the views of the authors and may not
   reflect the opinions or views of the NIH or ABCD consortium
   investigators. The ABCD data repository grows and changes over time. The
   ABCD data used in this report came from NIMH Data Archive Digital Object
   Identifier DOI 10.15154/1519007. DOIs can be found at
   https://nda.nih.gov/study.html?id1/4901. This work was supported in part
   by U01 DA041174 (to B.J.C.) and R01DK097399-01 (to K.M.R.) . The funders
   had no role in study design, data collection, and analysis, decision to
   publish, or preparation of the manuscript.},
Number-of-Cited-References = {58},
Times-Cited = {9},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {J. Adolesc. Health},
Doc-Delivery-Number = {1T4GD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000804688300016},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000885328900001,
Author = {Rat, Juliette and Mouthereau, Frederic and Brichau, Stephanie and
   Vacherat, Arnaud and Fillon, Charlotte and Gautheron, Cecile},
Title = {Timing and distribution of exhumation in the Ebro basin reveal a
   plate-scale 10 Ma geodynamic event},
Journal = {GLOBAL AND PLANETARY CHANGE},
Year = {2022},
Volume = {218},
Month = {NOV},
Abstract = {The interplays between deep geodynamic processes and Earth-surface
   erosion processes control the elevation and distribution of land masses,
   which in turn control environmental changes. These interactions can be
   best eval-uated in post-orogenic landscapes defined by decaying crustal
   deformation. This is the case of the Iberia peninsula where a growing
   body of geological evidence suggests the existence of a post-orogenic
   erosion around 10 Ma, well documented across the Pyrenees. Different
   mechanisms have been proposed, including lithospheric and
   sublithospheric processes, and Earth-surface processes triggered by
   base-level change and/or climate forcing on erosion. Here, we focus on
   the Ebro basin, which was a closed basin that opened towards the
   Mediterranean in the late Miocene. The distribution and exact timing of
   erosion in the Ebro basin are, however, only partially known, and do not
   yet allow resolving the post-orogenic mechanisms involved. We present
   new (U-Th-Sm)/He dates on apatite obtained in sandstones distributed
   from the edges of the Ebro basin to its center. The results of the
   thermal modelling confirm that the exhumation of the Ebro Basin took
   place between 12 and 6 Ma, or around 10 Ma when accounting for model
   uncertainties. Reconstruction of the sediment infill reveals that the
   late Miocene post-orogenic deposits were the thickest, between 1 and 1.6
   km, near the topographic front of adjacent mountain ranges and were the
   thinnest, approximately 300 m, in the center. The exhumation in the Ebro
   basin occurred after shortening has stopped, and before the Messinian
   Salinity Crisis. It is consistent with the wide-spread 10 Ma-exhumation
   event documented throughout Iberia, from the Aquitaine basin to the
   Betic Cordillera, and provides evidence of large-scale lithospheric and
   sublithospheric processes that coincide with the cessation of slab
   retreat in the West Mediterranean. We propose that a plate-scale uplift
   driven by deep-seated processes is the main cause of the Ebro basin
   incision. The response of the landscape to this geodynamically
   controlled erosion event led to a complex tectonic reorganization, e.g.
   along the strike of the Pyrenees, environmental changes in the
   Mediterranean, leading to the Messinian Salinity Crisis, and faunal
   turnover over Iberia.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Mouthereau, F (Corresponding Author), Univ Paul Sabatier, Geosci Environm Toulouse, GET, UMR 5563, Toulouse, France.
   Rat, Juliette; Mouthereau, Frederic; Brichau, Stephanie; Vacherat, Arnaud, Univ Paul Sabatier, Geosci Environm Toulouse, GET, UMR 5563, Toulouse, France.
   Fillon, Charlotte, Ctr Sci \& Tech Jean Feger, TotalEnergies SE, Pau, France.
   Gautheron, Cecile, Univ Paris Saclay, GEOPS, CNRS, Orsay, France.},
DOI = {10.1016/j.gloplacha.2022.103973},
EarlyAccessDate = {OCT 2022},
Article-Number = {103973},
ISSN = {0921-8181},
EISSN = {1872-6364},
Keywords = {Thermochronology; Exhumation; Topography; Basin; Mountain belts},
Keywords-Plus = {PARTICLE STOPPING DISTANCES; BASQUE-CANTABRIAN BASIN; DRAINAGE
   REORGANIZATION; STRUCTURAL EVOLUTION; TECTONIC INVERSION; GIBRALTAR ARC;
   WESTERN; PYRENEES; MARGIN; TROUGH},
Research-Areas = {Physical Geography; Geology},
Web-of-Science-Categories  = {Geography, Physical; Geosciences, Multidisciplinary},
Author-Email = {frederic.mouthereau@get.omp.eu},
Affiliations = {Centre National de la Recherche Scientifique (CNRS); CNRS - National
   Institute for Earth Sciences \& Astronomy (INSU); Universite de
   Toulouse; Universite Toulouse III - Paul Sabatier; Institut de Recherche
   pour le Developpement (IRD); Total SA; Centre Scientifique et Technique
   Jean Feger (CSTJF); Centre National de la Recherche Scientifique (CNRS);
   Universite Paris Saclay},
ResearcherID-Numbers = {Brichau, Stephanie S/L-6625-2017},
ORCID-Numbers = {Brichau, Stephanie S/0000-0002-8073-7103},
Funding-Acknowledgement = {TOTAL; BRGM; CNRS},
Funding-Text = {This paper is a contribution of Orogen, a tripartite project funded by
   TOTAL, BRGM and CNRS. It benefited from discussions along the course of
   the project with the Orogen Community. The authors would like to
   gratefully acknowledge Rosella Pinna-Jamme for the AHe analyses at
   GEOPS. We thank Christoph von Hagke, Tomas Capaldi and Nicolas
   Perez-Consuegra for insightful comments on the manuscript. Supple-
   mentary materials 1 and 2 are also accessible online in an open data
   repository https://doi.org/10.5281/zenodo.7089174.},
Number-of-Cited-References = {98},
Times-Cited = {3},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Glob. Planet. Change},
Doc-Delivery-Number = {6H3FA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000885328900001},
DA = {2024-01-15},
}

@article{ WOS:001014710900001,
Author = {Appleton, Katherine M. and Adams, Catherine},
Title = {A role for enjoyment for encouraging fruit consumption},
Journal = {APPETITE},
Year = {2023},
Volume = {187},
Month = {AUG 1},
Abstract = {This work investigated the value of highlighting the enjoyment conferred
   by fruit for encouraging fruit con-sumption. Study 1 investigated the
   effects on fruit consumption of visualizing eating fruit that was either
   enjoyable, not enjoyable, or was unassociated with enjoyment. Study 2
   investigated the effects on fruit con-sumption of health promotion
   posters that featured either enjoyable or less enjoyable fruit. Both
   studies used an independent-groups design, where young adults (Study 1,
   N = 142; Study 2, N = 221) were randomized to conditions, and outcomes:
   intentions to consume fruit, attitudes towards fruit, immediate fruit
   selection, sub-sequent fruit consumption; and a range of characteristics
   likely to be associated with fruit and vegetable con-sumption were
   assessed. In Study 1, higher intentions to consume fruit and more
   positive attitudes towards fruit were associated with higher likely
   enjoyment of the fruit visualized, higher fruit liking in general and
   higher fruit-related self-efficacy (smallest Beta = 0.270, p = 0.02). In
   Study 2, similar effects were found for likely enjoyment of the fruit
   featured on a poster; higher likely enjoyment also predicted greater
   immediate fruit se-lection (smallest Beta = 0.122, p = 0.03). These
   outcomes were also associated with variables often associated with fruit
   and vegetable consumption. Subsequent fruit consumption was only
   associated with past fruit con-sumption (smallest Beta = 0.340, p =
   0.05). These two studies (Study 1 using visualisation, Study 2 using
   health promotion posters) highlight a role for enjoyment for encouraging
   fruit consumption. The value of enjoyment and the simplicity of the
   poster intervention particularly should be noted.},
Publisher = {ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD},
Address = {24-28 OVAL RD, LONDON NW1 7DX, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Appleton, KM (Corresponding Author), Bournemouth Univ, Res Ctr Behav Change, Dept Psychol, Poole House,Farm Barrow, Poole BH12 5BB, England.
   Appleton, Katherine M., Bournemouth Univ, Dept Psychol, Poole, England.
   Appleton, Katherine M.; Adams, Catherine, Queens Univ, Sch Psychol, Belfast, North Ireland.
   Adams, Catherine, NICTU, Belfast, North Ireland.
   Appleton, Katherine M., Bournemouth Univ, Res Ctr Behav Change, Dept Psychol, Poole House,Farm Barrow, Poole BH12 5BB, England.},
DOI = {10.1016/j.appet.2023.106609},
EarlyAccessDate = {JUN 2023},
Article-Number = {106609},
ISSN = {0195-6663},
EISSN = {1095-8304},
Keywords = {Enjoyment; Fruit; Visualisation; Health promotion posters; Consumption
   behaviours},
Keywords-Plus = {VEGETABLE CONSUMPTION; SELF-EFFICACY; HEALTH-PROMOTION; PLANNED
   BEHAVIOR; FOOD CHOICE; SOCIAL SUPPORT; HABIT STRENGTH; LIKING; ADULTS;
   METAANALYSIS},
Research-Areas = {Behavioral Sciences; Nutrition \& Dietetics},
Web-of-Science-Categories  = {Behavioral Sciences; Nutrition \& Dietetics},
Author-Email = {k.appleton@bournemouth.ac.uk},
Affiliations = {Bournemouth University; Queens University Belfast; Bournemouth
   University},
ORCID-Numbers = {Appleton, Katherine/0000-0001-7045-3564},
Funding-Acknowledgement = {Department of Psychology, Bournemouth University, UK},
Funding-Text = {Data are available from the corresponding author on request, and held in
   Bournemouth University Open Data Repository BoRDAR. Part of this work
   was undertaken while both authors were employed by Queen's University,
   Belfast, UK; the latter part was undertaken after the first author had
   moved to Bournemouth University, UK. This latter part was supported by
   the Department of Psychology, Bournemouth University, UK. Grateful
   thanks are also extended to Tessa Harris, Lena Kessler, Charlotte Newton
   and Anna Stevens, Bournemouth University, for help with data collection.},
Number-of-Cited-References = {76},
Times-Cited = {1},
Usage-Count-Last-180-days = {8},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Appetite},
Doc-Delivery-Number = {K2HV0},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001014710900001},
OA = {Green Published, hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000746900400001,
Author = {Algaba, J. C. and Anczarski, J. and Asada, K. and Balokovic, M. and
   Chandra, S. and Cui, Y-Z and Falcone, A. D. and Giroletti, M. and Goddi,
   C. and Hada, K. and Haggard, D. and Jorstad, S. and Kaur, A. and
   Kawashima, T. and Keating, G. and Kim, J-Y and Kino, M. and Komossa, S.
   and Kravchenko, V, E. and Krichbaum, T. P. and Lee, S-S and Lu, R-S and
   Lucchini, M. and Markoff, S. and Neilsen, J. and Nowak, M. A. and Park,
   J. and Principe, G. and Ramakrishnan, V and Reynolds, M. T. and Sasada,
   M. and Savchenko, S. S. and Williamson, K. E. and Akiyama, Kazunori and
   Alberdi, Antxon and Alef, Walter and Anantua, Richard and Azula, Rebecca
   and Baczko, Anne-Kathrin and Ball, David and Barrett, John and Bintley,
   Dan and Benson, Bradford A. and Blackburn, Lindy and Blundell, Raymond
   and Boland, Wilfred and Bouman, Katherine L. and Bower, Geoffrey C. and
   Boyc, Hope and Bremer, Michael and Brinkerink, Christiaan D. and
   Brissenden, Roger and Britzen, Silke and Broderick, Avery E. and
   Broguiere, Dominique and Bronzwaer, Thomas and Byun, Do-Young and
   Carlstrom, John E. and Chael, Andrew and Chan, Chi-kwan and Chatterjee,
   Shami and Chatterjee, Koushik and Chen, Ming-Tang and Chen, Yongjun and
   Chesler, Paul M. and Cho, Ilje and Christian, Pierre and Conway, John E.
   and Cordes, James M. and Crawford, Thomas M. and Crew, Geoffrey B. and
   Cruz-Osorio, Alejandro and Davelaar, Jordy and De Laurentis,
   Mariafelicia and Deane, Roger and Dempsey, Jessica and Desvignes,
   Gregory and Dexter, Jason and Doeleman, Sheperd S. and Eatough, Ralph P.
   and Falcke, Heino and Farah, Joseph and Fish, Vincent L. and Fomalont,
   Ed and Ford, H. Alyson and Fraga-Encinas, Raquel and Friberg, Per and
   Fromm, Christian M. and Fuentes, Antonio and Galison, Peter and Gammie,
   Charles F. and Garcia, Roberto and Gentaz, Olivier and Georgiev, Boris
   and Gold, Roman and Gomez, Jose L. and Gomez-Ruiz, Arturo I. and Gu,
   Minfeng and Gurwell, Mark and Hecht, Michael H. and Hesper, Ronald and
   Ho, Luis C. and Ho, Paul and Honma, Mareki and Huang, Chih-Wei L. and
   Huang, Lei and Hughes, David H. and Ikeda, Shiro and Inoue, Makoto and
   Issaoun, Sara and James, David J. and Jannuzi, Buell T. and Janssen,
   Michael and Jeter, Britton and Jiang, Wu and Jimenez-Rosales, Alejandra
   and Johnson, Michael D. and Jung, Taehyun and Karami, Mansour and
   Karuppusamy, Ramesh and Kettenis, Mark and Kim, Dong-Jin and Kim,
   Jongsoo and Kim, Junhan and Koay, Jun Yi and Kofuji, Yutaro and Koch,
   Patrick M. and Koyama, Shoko and Kramer, Michael and Kramer, Carsten and
   Kuo, Cheng-Yu and Lauer, Tod R. and Levis, Aviad and Li, Yan-Rong and
   Li, Zhiyuan and Lindqvist, Michael and Lico, Rocco and Lindahl, Greg and
   Liu, Jun and Liu, Kuo and Liuzzo, Elisabetta and Lo, Wen-Ping and
   Lobanov, Andrei P. and Loinard, Laurent and Lonsdale, Colin and
   MacDonald, Nicholas R. and Mao, Jirong and Marchili, Nicola and Marrone,
   Daniel P. and Marscher, Alan P. and Marti-Vidal, Ivan and Matsushita,
   Satoki and Matthews, Lynn D. and Medeiros, Lia and Menten, Karl M. and
   Mizuno, Izumi and Mizuno, Yosuke and Moran, James M. and Moriyama,
   Kotaro and Moscibrodzka, Monika and Mueller, Cornelia and Musoke, Gibwa
   and Mejias, Alejandro Mus and Nagai, Hiroshi and Nagar, Neil M. and
   Nakamura, Masanori and Narayan, Ramesh and Narayanan, Gopal and
   Natarajan, Iniyan and Nathanail, Antonios and Neri, Roberto and Ni,
   Chunchong and Noutsos, Aristeidis and Okino, Hiroki and Olivares, Hector
   and Ortiz-Leon, Gisela N. and Oyama, Tomoaki and Ozel, Feryal and
   Palumbo, Daniel C. M. and Patel, Nimesh and Pen, Ue-Li and Pesce,
   Dominic W. and Pietu, Vincent and Plambeck, Richard and PopStefanija,
   Aleksandar and Porth, Oliver and Potzl, Felix M. and Prather, Ben and
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   Event Horizon Telescope and Event Horizon Telescope and Fermi Large Area
   Telescope and HESS Collaboration and HESS Collaboration and MAGIC
   Collaboration and MAGIC Collaboration and VERITAS Collaboration and
   VERITAS Collaboration and EAVN Collaboration},
Title = {Broadband Multi-wavelength Properties of M87 during the 2017 Event
   Horizon Telescope Campaign},
Journal = {ASTROPHYSICAL JOURNAL LETTERS},
Year = {2021},
Volume = {911},
Number = {1},
Month = {APR},
Abstract = {In 2017, the Event Horizon Telescope (EHT) Collaboration succeeded in
   capturing the first direct image of the center of the M87 galaxy. The
   asymmetric ring morphology and size are consistent with theoretical
   expectations for a weakly accreting supermassive black hole of mass
   similar to 6.5 x 10(9) M-circle dot. The EHTC also partnered with
   several international facilities in space and on the ground, to arrange
   an extensive, quasi-simultaneous multi-wavelength campaign. This Letter
   presents the results and analysis of this campaign, as well as the
   multi-wavelength data as a legacy data repository. We captured M87 in a
   historically low state, and the core flux dominates over HST-1 at high
   energies, making it possible to combine core flux constraints with the
   more spatially precise very long baseline interferometry data. We
   present the most complete simultaneous multi-wavelength spectrum of the
   active nucleus to date, and discuss the complexity and caveats of
   combining data from different spatial scales into one broadband
   spectrum. We apply two heuristic, isotropic leptonic single-zone models
   to provide insight into the basic source properties, but conclude that a
   structured jet is necessary to explain M87's spectrum. We can exclude
   that the simultaneous gamma-ray emission is produced via inverse Compton
   emission in the same region producing the EHT mm-band emission, and
   further conclude that the gamma-rays can only be produced in the inner
   jets (inward of HST-1) if there are strongly particle-dominated regions.
   Direct synchrotron emission from accelerated protons and secondaries
   cannot yet be excluded.},
Publisher = {IOP Publishing Ltd},
Address = {TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Algaba, JC (Corresponding Author), Univ Malaya, Fac Sci, Dept Phys, Kuala Lumpur 50603, Malaysia.
   Algaba, J. C., Univ Malaya, Fac Sci, Dept Phys, Kuala Lumpur 50603, Malaysia.
   Anczarski, J.; Neilsen, J., Villanova Univ, Dept Phys, 800 E Lancaster Ave, Villanova, PA 19085 USA.
   Asada, K., Acad Sinica, Inst Astron \& Astrophys, 11F Astron Math Bldg,AS NTU 1,Sec 4,Roosevelt Rd, Taipei 10617, Taiwan.
   Balokovic, M., Yale Ctr Astron \& Astrophys, 52 Hillhouse Ave, New Haven, CT 06511 USA.
   Balokovic, M.; Park, J., Yale Univ, Dept Phys, POB 2018120, New Haven, CT 06520 USA.
   Chandra, S., North West Univ, Ctr Space Res, ZA-2520 Potchefstroom, South Africa.
   Cui, Y-Z; Hada, K., Grad Univ Adv Studies SOKENDAI, Dept Astron Sci, 2-21-1 Osawa, Mitaka, Tokyo 1818588, Japan.
   Cui, Y-Z; Hada, K., Mizusawa VLBI Observ, 2-12 Hoshigaoka, Oshu, Iwate 0230861, Japan.
   Falcone, A. D.; Kaur, A., Penn State Univ, Dept Astron \& Astrophys, 525 Davey Lab, University Pk, PA 16802 USA.
   Giroletti, M.; Kravchenko, E., V; Principe, G., INAF Ist Radioastron, Via P Gobetti 101, I-40129 Bologna, Italy.
   Goddi, C., Radboud Univ Nijmegen, Inst Math Astrophys \& Particle Phys IMAPP, Dept Astrophys, POB 9010, NL-6500 GL Nijmegen, Netherlands.
   Goddi, C., Leiden Univ, Leiden Observ Allegro, POB 9513, NL-2300 RA Leiden, Netherlands.
   Haggard, D., McGill Univ, Dept Phys, 3600 Univ St, Montreal, PQ H3A 2T8, Canada.
   Haggard, D., McGill Univ, McGill Space Inst, 3550 Univ St, Montreal, PQ H3A 2A7, Canada.
   Jorstad, S.; Williamson, K. E., Boston Univ, Inst Astrophys Res, 725 Commonwealth Ave, Boston, MA 02215 USA.
   Jorstad, S., St Petersburg Univ, Astron Inst, Univ Skij Pr 28, St Petersburg 198504, Russia.
   Kawashima, T., Univ Tokyo, Inst Cosm Ray Res, 5-1-5 Kashiwanoha, Kashiwa, Chiba 2778582, Japan.
   Keating, G., Harvard \& Smithsonian, Ctr Astrophys, 60 Garden St, Cambridge, MA 02138 USA.
   Kim, J-Y; Lee, S-S, Korea Astron \& Space Sci Inst, Daedeok Daero 776, Daejeon 34055, South Korea.
   Kim, J-Y; Komossa, S.; Krichbaum, T. P.; Lu, R-S, Max Planck Inst Radioastron, Hugel 69, D-53121 Bonn, Germany.
   Kino, M.; Sasada, M., Natl Astron Observ Japan, 2-21-1 Osawa, Mitaka, Tokyo 1818588, Japan.
   Kino, M., Kogakuin Univ Technol \& Engn, Acad Support Ctr, 2665-1 Nakano, Hachioji, Tokyo 1920015, Japan.
   Kravchenko, E., V; Park, J., Moscow Inst Phys \& Technol, Inst Sky Per 9, Dolgoprudnyi 141700, Moscow Region, Russia.
   Kravchenko, E., V, Lebedev Phys Inst, Astro Space Ctr, Profsouznaya 84-32, Moscow 117997, Russia.
   Lu, R-S, Chinese Acad Sci, Shanghai Astron Observ, 80 Nandan Rd, Shanghai 200030, Peoples R China.
   Lu, R-S, Chinese Acad Sci, Key Lab Radio Astron, Nanjing 210008, Peoples R China.
   Lucchini, M.; Markoff, S., Univ Amsterdam, API Anton Pannekoek Inst Astron, Sci Pk 904, NL-1098 XH Amsterdam, Netherlands.
   Markoff, S., Univ Amsterdam, GRAPPA Gravitat \& AstroParticle Phys Amsterdam, Sci Pk 904, NL-1098 XH Amsterdam, Netherlands.
   Nowak, M. A., Washington Univ, Phys Dept, CB 1105, St Louis, MO 63130 USA.
   Park, J., Acad Sinica, Inst Astron \& Astrophys, POB 23-141, Taipei 10617, Taiwan.
   Park, J., Seoul Natl Univ, Dept Phys \& Astron, Seoul 08826, South Korea.
   Principe, G., Univ Trieste, Dipartimento Fis, I-34127 Trieste, Italy.
   Principe, G., Ist Nazl Fis Nucl, Sez Trieste, I-34127 Trieste, Italy.
   Ramakrishnan, V, Univ Concepcion, Astron Dept, Casilla 160-C, Concepcion, Chile.
   Reynolds, M. T., Univ Michigan, 1085 S Univ Ave, Ann Arbor, MI 48109 USA.
   Sasada, M., Hiroshima Univ, Hiroshima Astrophys Sci Ctr, 1-3-1 Kagamiyama, Higashihiroshima, Hiroshima 7398526, Japan.
   Savchenko, S. S., St Petersburg State Univ, 7-9 Univ Skaya Nab, St Petersburg 199034, Russia.
   Savchenko, S. S., Russian Acad Sci, Special Astrophys Observ, Nizhnii Arkhyz 369167, Russia.},
DOI = {10.3847/2041-8213/abef71},
Article-Number = {L11},
ISSN = {2041-8205},
EISSN = {2041-8213},
Keywords = {Active galactic nuclei; Radio cores; Low-luminosity active galactic
   nuclei; High energy astrophysics; Astrophysical black holes; Accretion},
Keywords-Plus = {SUPERMASSIVE BLACK-HOLE; LARGE-AREA TELESCOPE; SGR A-ASTERISK; ACTIVE
   GALACTIC NUCLEI; VIRGO-CLUSTER SURVEY; GAMMA-RAY EMISSION; GALAXY M 87;
   HIGH-RESOLUTION; JET BASE; VERITAS OBSERVATIONS},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Affiliations = {Universiti Malaya; Villanova University; Academia Sinica - Taiwan; Yale
   University; Yale University; North West University - South Africa;
   Graduate University for Advanced Studies - Japan; Pennsylvania
   Commonwealth System of Higher Education (PCSHE); Pennsylvania State
   University; Pennsylvania State University - University Park; Istituto
   Nazionale Astrofisica (INAF); Radboud University Nijmegen; Leiden
   University; Leiden University - Excl LUMC; McGill University; McGill
   University; Boston University; Saint Petersburg State University;
   University of Tokyo; Smithsonian Institution; Korea Astronomy \& Space
   Science Institute (KASI); Max Planck Society; National Institutes of
   Natural Sciences (NINS) - Japan; National Astronomical Observatory of
   Japan (NAOJ); Moscow Institute of Physics \& Technology; Russian Academy
   of Sciences; Russian Academy of Science Lebedev Physical Institute;
   Chinese Academy of Sciences; Shanghai Astronomical Observatory, CAS;
   Chinese Academy of Sciences; University of Amsterdam; University of
   Amsterdam; Washington University (WUSTL); Academia Sinica - Taiwan;
   Seoul National University (SNU); University of Trieste; Istituto
   Nazionale di Fisica Nucleare (INFN); Universidad de Concepcion;
   University of Michigan System; University of Michigan; Hiroshima
   University; Saint Petersburg State University; Russian Academy of
   Sciences; Special Astrophysics Observatory of the Russian Academy of
   Sciences},
ResearcherID-Numbers = {Gliwny, Paweł/AAP-4554-2021
   Covino, Stefano/AAQ-5188-2021
   Loporchio, Serena/ABI-7619-2020
   Zhao, Guang-Yao/AAA-7324-2019
   sun, he/IYJ-6174-2023
   Reimer, Olaf/A-3117-2013
   Gómez, José L/C-4195-2008
   Venter, Christo/E-6884-2011
   Goddi, Ciriaco/AAN-4033-2021
   Wielgus, Maciej/J-9736-2012
   Giroletti, Marcello/ACH-5368-2022
   Casanova, Sabrina/AAG-5332-2021
   MAURIN, Guillaume GM/G-7435-2015
   Wielgus, Maciek/JEF-6647-2023
   Ramakrishnan, Venkatessh/C-8628-2017
   Chen, Ming-Tang/ABC-7461-2020
   Ikeda, Shiro/E-1736-2016
   Wierzcholska, Alicja/AAV-2997-2021
   Rosillo, Mireia Nievas/Q-1808-2019
   Ho, Paul/AAZ-5108-2020
   Reichherzer, Patrick/GLV-4438-2022
   Rezzolla, Luciano/JPK-1036-2023
   Koch, Patrick/AAV-3373-2021
   Park, Jongho/JFB-2747-2023
   Molina, Edgar/B-8037-2019
   Ros, Eduardo/B-1014-2015
   Kawashima, Tomohisa/GYD-8953-2022
   Algaba, Juan Carlos/AAB-4526-2022
   Moreno Baltà, Victòria/K-3379-2015
   Doro, Michele/F-9458-2012
   Pohl, Martin/P-4920-2017
   Kim, Jae-Young/IUO-6466-2023
   Cortina, Juan/C-2783-2017
   Barbosa Martins, Victor/C-3696-2016
   Hassan, Tarek/T-9225-2019
   Cruz Osorio, Alejandro/GQQ-8823-2022
   Baghmanyan, Vardan/AAV-9113-2021
   Pen, Ue-Li/AAX-6083-2021
   Cerruti, Matteo/AAA-6400-2020
   Karjalainen, Marie/AAA-4957-2019
   Principe, Giacomo/AHD-0733-2022
   Peron, Giada/AAR-2278-2021
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   Lobanov, Andrei P./G-5891-2014
   FERRARA, Giovanna/GSI-5734-2022
   Baquero Larriva, Andres/IAN-0566-2023
   Kravchenko, Evgeniya Vasilyevna/M-7464-2013
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   Koay, Jun Yi/E-4952-2015
   浅田圭一, Keiichi ASADA/ABC-2456-2020
   Angüner, Ekrem Oğuzhan/ISU-3344-2023
   Horns, Dieter/ABE-9516-2020
   Jin, Weidong/ABU-9003-2022
   Daniel, Michael K/A-2903-2010
   Barres de Almeida, Ulisses/V-4025-2019
   Bianchi, Marco Emilio/K-3417-2018
   Sakai, Nobuyuki/GRX-6802-2022
   Spencer, Samuel Timothy/JAC-6182-2023
   Funk, Stefan/B-7629-2015
   Morcuende, Daniel/B-7240-2018
   Rao, Ramprasad/L-2115-2017
   Lombardi, Saverio/Q-2818-2018
   Chilingarian, Ashot/B-1901-2014
   Nieto, Daniel/J-7250-2015
   Verguilov, Vassil/A-5885-2014
   giglietto, nicola/I-8951-2012
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   Godinovic, Nikola/G-6124-2017
   Delgado, Jordi/F-8146-2016
   Blanch Bigas, Oscar/N-7147-2016
   Komin, Nukri/J-6781-2015
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   Loporchio, Serena/0000-0003-4457-5431
   Zhao, Guang-Yao/0000-0002-4417-1659
   Reimer, Olaf/0000-0001-6953-1385
   Gómez, José L/0000-0003-4190-7613
   Venter, Christo/0000-0002-2666-4812
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   Giroletti, Marcello/0000-0002-8657-8852
   Casanova, Sabrina/0000-0002-6144-9122
   MAURIN, Guillaume GM/0000-0002-2096-0450
   Ramakrishnan, Venkatessh/0000-0002-9248-086X
   Chen, Ming-Tang/0000-0001-6573-3318
   Ikeda, Shiro/0000-0002-2462-1448
   Wierzcholska, Alicja/0000-0003-4472-7204
   Rosillo, Mireia Nievas/0000-0002-8321-9168
   Ho, Paul/0000-0002-3412-4306
   Reichherzer, Patrick/0000-0003-4513-8241
   Koch, Patrick/0000-0003-2777-5861
   Park, Jongho/0000-0001-6558-9053
   Molina, Edgar/0000-0003-1204-5516
   Ros, Eduardo/0000-0001-9503-4892
   Kawashima, Tomohisa/0000-0001-8527-0496
   Algaba, Juan Carlos/0000-0001-6993-1696
   Moreno Baltà, Victòria/0000-0002-8358-2098
   Doro, Michele/0000-0001-9104-3214
   Pohl, Martin/0000-0001-7861-1707
   Kim, Jae-Young/0000-0001-8229-7183
   Cortina, Juan/0000-0003-4576-0452
   Barbosa Martins, Victor/0000-0002-5085-8828
   Hassan, Tarek/0000-0002-4758-9196
   Baghmanyan, Vardan/0000-0003-0477-1614
   Pen, Ue-Li/0000-0003-2155-9578
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   Karjalainen, Marie/0000-0003-0751-3231
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   Baquero Larriva, Andres/0000-0002-1757-5826
   Kravchenko, Evgeniya Vasilyevna/0000-0003-4540-4095
   Colak, Sidika Merve/0000-0001-7793-3106
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   Shao, Lijing/0000-0002-1334-8853
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Funding-Acknowledgement = {Malaysian Fundamental Research Grant Scheme (FRGS)
   {[}FRGS/1/2019/STG02/UM/02/6]; YCAA Prize Postdoctoral Fellowship; Black
   Hole Initiative at Harvard University - Gordon and Betty Moore
   Foundation {[}GBMF8273]; Templeton Foundation; South African Research
   Chairs Initiative of the Department of Science and Innovation and the
   National Research Foundation of South Africa {[}64789]; JSPS KAKENHI
   {[}JJP18H03721, JP19H01943, JP18KK0090, JP18K13594, JP19H01908,
   JP19H01906, JP19K14761]; Mitsubishi Foundation {[}201911019]; Natural
   Sciences and Engineering Research Council of Canada (NSERC) Discovery
   Grant; Canada Research Chairs program; MEXT; JICFuS; Max Planck Partner
   Group of the MPG; Key Program of the National Natural Science Foundation
   of China {[}11933007]; Research Program of Fundamental and Frontier
   Sciences, CAS {[}ZDBS-LY-SLH011]; NWO (Netherlands Organisation for
   Scientific Research) VICI award {[}639.043.513]; SAO award
   {[}DD7-18089X]; NASA award {[}80NSSC20K0645]; Korean National Research
   Foundation (NRF) via Global PhD Fellowship grant {[}2014H1A2A1018695];
   East Asia Core Observatories Association; Academy of Finland {[}274477,
   284495, 312496, 315721, 320045]; Agencia Nacional de Investigacion y
   Desarrollo (ANID), Chile {[}NCN19\_058]; FONDECYT {[}3190878]; Alexander
   von Humboldt Stiftung; Black Hole Initiative at Harvard University from
   the John Templeton Foundation {[}60477]; China Scholarship Council;
   Consejo Nacional de Ciencia y Tecnologia (CONACYT, Mexico) {[}104497,
   275201, 279006, 281692]; Delaney Family via the Delaney Family John A.
   Wheeler Chair at Perimeter Institute; Direccion General de Asuntos del
   Personal Academico-Universidad Nacional Autonoma de Mexico (DGAPA-UNAM,
   project) {[}IN112417]; European Research Council Synergy Grant
   ``BlackHoleCam: Imaging the Event Horizon of Black Holes{''} {[}610058];
   Generalitat Valenciana postdoctoral grant {[}APOSTD/2018/177]; GenT
   Program {[}CIDEGENT/2018/021]; Gordon and Betty Moore Foundation
   {[}GBMF-3561, GBMF-5278, GBMF 947]; Istituto Nazionale di Fisica
   Nucleare (INFN) sezione di Napoli, iniziative specifiche TEONGRAV;
   International Max Planck Research School for Astronomy and Astrophysics
   at the Universities of Bonn and Cologne; Japanese Government
   (Monbukagakusho: MEXT) Scholarship; Japan Society for the Promotion of
   Science (JSPS) {[}JP17J08829]; Key Research Program of Frontier
   Sciences, Chinese Academy of Sciences (CAS) {[}QYZDJ-SSW-SLH057,
   QYZDJ-SSW-SYS008]; Leverhulme Trust Early Career Research Fellowship;
   Max-Planck-Gesellschaft (MPG); CAS; MEXT/JSPS KAKENHI {[}JP18K13594,
   18KK0090, JP18K03656, JP18H03721, 18K03709, 18H01245, 25120007]; MIT
   International Science and Technology Initiatives (MISTI) Funds; Ministry
   of Science and Technology (MOST) of Taiwan {[}1052112-M-001-025-MY3,
   106-2112-M-001-011, 106-2119-M-001027, 107-2119-M-001-017,
   107-2119-M-001-020, 107-2119-M110-005, 108-2112-M-001-048,
   109-2124-M-001-005]; National Aeronautics and Space Administration
   (NASA) {[}80NSSC20K1567]; Space Telescope Science Institute
   {[}HST-HF2-51431.001-A]; Association of Universities for Research in
   Astronomy, Inc., for NASA {[}DD7-18089X, 80NSSC20K0645, NAS5-26555];
   National Institute of Natural Sciences (NINS) of Japan; National Key
   Research and Development Program of China {[}2016YFA0400704,
   2016YFA0400702]; National Science Foundation (NSF) {[}AST-0096454,
   AST-0352953, AST-0521233, AST0705062, AST-0905844, AST-0922984,
   AST-1126433, AST1140030, DGE-1144085, AST-1207704, AST-1207730,
   AST1207752, MRI-1228509, OPP-1248097]; Natural Science Foundation of
   China {[}11573051, 11633006, 11650110427, 10625314, 11721303, 11725312,
   11991053]; Natural Sciences and Engineering Research Council of Canada
   (NSERC); NSERC Alexander Graham Bell Canada Graduate
   Scholarships-Doctoral Program); National Research Foundation of Korea
   {[}NRF2015H1A2A1033752, 2015-R1D1A1A01056807, NRF-2015H1D3A1066561];
   Netherlands Organization for Scientific Research (NWO) VICI award
   {[}639.043.513]; Spinoza Prize {[}SPI 78-409]; New Scientific Frontiers
   with Precision Radio Interferometry Fellowship - South African Radio
   Astronomy Observatory (SARAO); Swedish Research Council {[}2017-00648];
   Government of Canada through the Department of Innovation, Science and
   Economic Development; Province of Ontario through the Ministry of
   Research, Innovation and Science; Spanish Ministerio de Economia y
   Competitividad {[}PGC2018-098915-B-C21, AYA201680889-P]; State Agency
   for Research of the Spanish MCIU through the ``Center of Excellence
   Severo Ochoa{''} award for the Instituto de Astrofisica de Andalucia
   {[}SEV-2017-0709]; Toray Science Foundation; US Department of Energy
   (USDOE) through the Los Alamos National Laboratory {[}89233218CNA
   000001]; European Union's Horizon 2020 research and innovation program
   {[}730562]; ALMA North America Development Fund; Academia Sinica;
   Chandra {[}TM6-17006X]; GenT Program (Generalitat Valenciana) Project
   {[}CIDEGENT/2018/021]; CyVerse; Compute Ontario; Compute Canada; ALMA
   {[}2016.1.01154.V]; Smithsonian Institution; National Key RAMP;D Program
   of China {[}2017YFA0402700]; Science and Technologies Facility Council
   (UK); Consejo Nacional de Ciencia y Tecnologia; CNRS (Centre National de
   la Recherche Scientifique, France); MPG (MaxPlanck-Gesellschaft,
   Germany); IGN (Instituto Geografico Nacional, Spain); State of Arizona;
   Kavli Foundation; EVN project {[}EH033]; KREONET (Korea Research
   Environment Open NETwork); Russian Science Foundation {[}20-62-46021];
   Istituto Nazionale di Astrofisica in Italy; Centre National d'Etudes
   Spatiales in France; DOE {[}DEAC02-76SF00515]; University of Namibia;
   German Ministry for Education and Research (BMBF); Max Planck Society;
   German Research Foundation (DFG) {[}SFB823/C4, SFB876/C3]; Helmholtz
   Association; Alexander von Humboldt Foundation; French Ministry of
   Higher Education, Research and Innovation; Centre National de la
   Recherche Scientifique {[}CNRS/IN2P3]; Commissariat a l'energie atomique
   et aux energies alternatives (CEA); U.K. Science and Technology
   Facilities Council (STFC); Knut and Alice Wallenberg Foundation;
   National Science Centre {[}2016/22/M/ST9/00382]; South African
   Department of Science and Technology and National Research Foundation;
   National Commission on Research, Science AMP;Technology of Namibia
   (NCRST); Austrian Federal Ministry of Education, Science and Research;
   Austrian Science Fund (FWF); Australian Research Council (ARC); Japan
   Society for the Promotion of Science; University of Amsterdam; EGI
   Federation; MPG; HGF; Italian INFN; INAF; Swiss National Fund SNF; ERDF
   under the Spanish Ministerio de Ciencia e Innovacion (MICINN)
   {[}FPA2017-87859-P, FPA2017-85668-P, FPA201782729-C6-5-R,
   FPA2017-90566-REDC, PID2019-104114RBC31, PID2019-104114RB-C32,
   PID2019-105510GB-C31, PID 2019-107847RB-C41, PID2019-107847RB-C42,
   PID2019107988GB-C22]; Indian Department of Atomic Energy; Japanese ICRR;
   University of Tokyo; Bulgarian Ministry of Education and Science;
   National RI Roadmap {[}DO1-268/16.12.2019]; Spanish Centro de Excelencia
   ``Severo Ochoa{''} {[}SEV-2016-0588, CEX2019000920-S]; Maria de Maeztu
   {[}CEX2019-000918-M]; Unidad de Excelencia ``Maria de Maeztu{''}
   {[}MDM-2015-050918-2]; ``la Caixa{''} Foundation
   {[}LCF/BQ/PI18/11630012]; CERCA program of the Generalitat de Catalunya;
   Croatian Science Foundation (HrZZ) {[}IP-2016-06-9782]; University of
   Rijeka {[}13.12.1.3.02]; Polish National Research Centre
   {[}UMO-2016/22/M/ST9/00382]; Brazilian MCTIC; CNPq; FAPERJ; U.S.
   Department of Energy Office of Science {[}DE-AC02-05CH11231]; U.S.
   National Science Foundation; NSERC in Canada; Helmholtz Association in
   Germany; the National Research Foundation (NRF) {[}AST-1310896,
   AST1337663, AST-1440254, AST-1555365, AST-1715061, AST1615796,
   AST-1716327, OISE-1743747, AST-1816420, AST2034306, ACI-1548562,
   DBI-0735191, DBI-1265383, DBI-1743442, PLR-1248097, PHY-1125897]; 
   {[}TGAST170024];  {[}TG-AST080026N];  {[}AST170028]},
Funding-Text = {J.-C.A acknowledges support from the Malaysian Fundamental Research
   Grant Scheme (FRGS) FRGS/1/2019/STG02/UM/02/6. M.B. acknowledges support
   from the YCAA Prize Postdoctoral Fellowship and the Black Hole
   Initiative at Harvard University, which is funded in part by the Gordon
   and Betty Moore Foundation (grant GBMF8273) and in part by the John
   Templeton Foundation. S.C. is supported by the South African Research
   Chairs Initiative (grant No. 64789) of the Department of Science and
   Innovation and the National Research Foundation of South Africa. K.H.
   acknowledges support from JSPS KAKENHI grant Nos. JJP18H03721,
   JP19H01943, JP18KK0090, and support from the Mitsubishi Foundation grant
   No. 201911019. D.H. acknowledges support from the Natural Sciences and
   Engineering Research Council of Canada (NSERC) Discovery Grant and the
   Canada Research Chairs program. T.K. acknowledges support from JSPS
   KAKENHI grant Nos. JP18K13594, JP19H01908, JP19H01906, MEXT as ``Program
   for Promoting Researches on the Supercomputer Fugaku{''} (Toward a
   unified view of the universe: from large scale structures to planets),
   MEXT as ``Priority Issue on post-K computer{''} (Elucidation of the
   Fundamental Laws and Evolution of the Universe) and JICFuS. A part of
   the calculations were carried out on the XC50 at the Center for
   Computational Astrophysics, National Astronomical Observatory of Japan.
   R.-S.L. is supported by the Max Planck Partner Group of the MPG and the
   CAS and acknowledges support from the Key Program of the National
   Natural Science Foundation of China(grant No. 11933007) and the Research
   Program of Fundamental and Frontier Sciences, CAS (grant No.
   ZDBS-LY-SLH011). M.L. and S.M. are thankful for support from an NWO
   (Netherlands Organisation for Scientific Research) VICI award, grant No.
   639.043.513. J.N. acknowledges support from SAO award DD7-18089X and
   NASA award 80NSSC20K0645. J.P. acknowledges financial support from the
   Korean National Research Foundation (NRF) via Global PhD Fellowship
   grant 2014H1A2A1018695 and support through the EACOA Fellowship awarded
   by the East Asia Core Observatories Association, which consists of the
   Academia Sinica Institute of Astronomy and Astrophysics, the National
   Astronomical Observatory of Japan, Center for Astronomical Mega-Science,
   Chinese Academy of Sciences, and the Korea Astronomy and Space Science
   Institute. M.S. acknowledges support from JSPS KAKENHI grant Nos.
   JP19K14761. The authors of the present Letter thank the following
   organizations and programs: the Academy of Finland (projects 274477,
   284495, 312496, 315721); Agencia Nacional de Investigacion y Desarrollo
   (ANID), Chile via NCN19\_058 (TITANs) and FONDECYT 3190878; the
   Alexander von Humboldt Stiftung; the Black Hole Initiative at Harvard
   University, through a grant (60477) from the John Templeton Foundation;
   the China Scholarship Council; Consejo Nacional de Ciencia y Tecnologia
   (CONACYT, Mexico, projects 104497, 275201, 279006, 281692); the Delaney
   Family via the Delaney Family John A.; r Wheeler Chair at Perimeter
   Institute; Direccion General de Asuntos del Personal
   Academico-Universidad Nacional Autonoma de Mexico (DGAPA-UNAM, project
   IN112417); the European Research Council Synergy Grant ``BlackHoleCam:
   Imaging the Event Horizon of Black Holes{''} (grant 610058); the
   Generalitat Valenciana postdoctoral grant APOSTD/2018/177 and GenT
   Program (project CIDEGENT/2018/021); the Gordon and Betty Moore
   Foundation (grants GBMF-3561, GBMF-5278); the Istituto Nazionale di
   Fisica Nucleare (INFN) sezione di Napoli, iniziative specifiche
   TEONGRAV; the International Max Planck Research School for Astronomy and
   Astrophysics at the Universities of Bonn and Cologne; the Japanese
   Government (Monbukagakusho: MEXT) Scholarship; the Japan Society for the
   Promotion of Science (JSPS) Grant-in-Aid for JSPS Research Fellowship
   (JP17J08829); the Key Research Program of Frontier Sciences, Chinese
   Academy of Sciences (CAS, grants QYZDJ-SSW-SLH057, QYZDJ-SSW-SYS008);
   the Leverhulme Trust Early Career Research Fellowship; the
   Max-Planck-Gesellschaft (MPG); the Max Planck Partner Group of the MPG
   and the CAS; the MEXT/JSPS KAKENHI (grants 18KK0090, JP18K13594,
   JP18K03656, JP18H03721, 18K03709, 18H01245, 25120007); the MIT
   International Science and Technology Initiatives (MISTI) Funds; the
   Ministry of Science and Technology (MOST) of Taiwan
   (1052112-M-001-025-MY3, 106-2112-M-001-011, 106-2119-M-001027,
   107-2119-M-001-017, 107-2119-M-001-020, 107-2119-M110-005,
   108-2112-M-001-048 and 109-2124-M-001-005); the National Aeronautics and
   Space Administration (NASA, Fermi Guest Investigator grant 80NSSC20K1567
   and Hubble Fellowship grant HST-HF2-51431.001-A awarded by the Space
   Telescope Science Institute, which is operated by the Association of
   Universities for Research in Astronomy, Inc., for NASA, under contract
   NAS5-26555, NuSTAR award 80NSSC20K0645, Chandra award DD7-18089X); the
   National Institute of Natural Sciences (NINS) of Japan; the National Key
   Research and Development Program of China (grant 2016YFA0400704,
   2016YFA0400702); the National Science Foundation (NSF, grants
   AST-0096454, AST-0352953, AST-0521233, AST0705062, AST-0905844,
   AST-0922984, AST-1126433, AST1140030, DGE-1144085, AST-1207704,
   AST-1207730, AST1207752, MRI-1228509, OPP-1248097, AST-1310896,
   AST1337663, AST-1440254, AST-1555365, AST-1715061, AST1615796,
   AST-1716327, OISE-1743747, AST-1816420, AST2034306); the Natural Science
   Foundation of China (grants 11573051, 11633006, 11650110427, 10625314,
   11721303, 11725312, 11991053); the Natural Sciences and Engineering
   Research Council of Canada (NSERC, including a Discovery Grant and the
   NSERC Alexander Graham Bell Canada Graduate Scholarships-Doctoral
   Program); the National Research Foundation of Korea (the Global PhD
   Fellowship Grant: grants NRF2015H1A2A1033752, 2015-R1D1A1A01056807, the
   Korea Research Fellowship Program: NRF-2015H1D3A1066561); the
   Netherlands Organization for Scientific Research (NWO) VICI award (grant
   639.043.; r 513) and Spinoza Prize SPI 78-409; the New Scientific
   Frontiers with Precision Radio Interferometry Fellowship awarded by the
   South African Radio Astronomy Observatory (SARAO), which is a facility
   of the National Research Foundation (NRF), an agency of the Department
   of Science and Innovation (DSI) of South Africa; the South African
   Research Chairs Initiative of the Department of Science and Innovation
   and National Research Foundation; the Onsala Space Observatory (OSO)
   national infrastructure, for the provisioning of its
   facilities/observational support (OSO receives funding through the
   Swedish Research Council under grant 2017-00648) the Perimeter Institute
   for Theoretical Physics (research at Perimeter Institute is supported by
   the Government of Canada through the Department of Innovation, Science
   and Economic Development and by the Province of Ontario through the
   Ministry of Research, Innovation and Science); the Spanish Ministerio de
   Economia y Competitividad (grants PGC2018-098915-B-C21, AYA201680889-P);
   the State Agency for Research of the Spanish MCIU through the ``Center
   of Excellence Severo Ochoa{''} award for the Instituto de Astrofisica de
   Andalucia (SEV-2017-0709); the Toray Science Foundation; the US
   Department of Energy (USDOE) through the Los Alamos National Laboratory
   (operated by Triad National Security, LLC, for the National Nuclear
   Security Administration of the USDOE (Contract 89233218CNA 000001)); the
   European Union's Horizon 2020 research and innovation program under
   grant agreement No. 730562 RadioNet; ALMA North America Development
   Fund; the Academia Sinica; Chandra TM6-17006X; the GenT Program
   (Generalitat Valenciana) Project CIDEGENT/2018/021. This work used the
   Extreme Science and Engineering Discovery Environment (XSEDE), supported
   by NSF grant ACI-1548562, and CyVerse, supported by NSF grants
   DBI-0735191, DBI-1265383, and DBI-1743442. XSEDE Stampede2 resource at
   TACC was allocated through TGAST170024 and TG-AST080026N. XSEDE
   JetStream resource at PTI and TACC was allocated through AST170028. The
   simulations were performed in part on the SuperMUC cluster at the LRZ in
   Garching, on the LOEWE cluster in CSC in Frankfurt, and on the HazelHen
   cluster at the HLRS in Stuttgart. This research was enabled in part by
   support provided by Compute Ontario (http://computeontario.ca), Calcul
   Quebec (http://www.calculquebec.ca) and Compute Canada
   (http://www.compute canada.ca). We thank the staff at the participating
   observatories, correlation centers, and institutions for their
   enthusiastic support. This Letter makes use of the following ALMA data:
   ADS/JAO.ALMA\#2016.1.01154.V. ALMA is a partnership of the European
   Southern Observatory (ESO; Europe, representing its member states), NSF,
   and National Institutes of Natural Sciences of Japan, together with
   National Research Council (Canada), Ministry of Science and Technology
   (MOST; Taiwan), Academia Sinica Institute of Astronomy and Astrophysics
   (ASIAA; Taiwan), and Korea Astronomy and Space Science Institute (KASI;
   Republic of Korea), in cooperation with the Republic of Chile. The Joint
   ALMA Observatory is operated by ESO, Associated Universities, Inc.
   (AUI)/NRAO, and the National Astronomical Observatory of Japan (NAOJ).
   The NRAO is a facility of the NSF operated under cooperative agreement
   by AUI. APEX is a collaboration between the Max-Planck-Institut fur
   Radioastronomie (Germany), ESO, and the Onsala Space Observatory
   (Sweden). The SMA is a joint project between the SAO and ASIAA and is
   funded by the Smithsonian Institution and the Academia Sinica.; r The
   JCMT is operated by the East Asian Observatory on behalf of the NAOJ,
   ASIAA, and KASI, as well as the Ministry of Finance of China, Chinese
   Academy of Sciences, and the National Key R\&D Program (No.
   2017YFA0402700) of China. Additional funding support for the JCMT is
   provided by the Science and Technologies Facility Council (UK) and
   participating universities in the UK and Canada. he LMT is a project
   operated by the Instituto Nacional de Astrofi ` sica, O ` ptica, y
   Electro ` nica (Mexico) and the University of Massachusetts at Amherst
   (USA), with financial support from the Consejo Nacional de Ciencia y
   Tecnologia and the National Science Foundation. The IRAM 30-m telescope
   on Pico Veleta, Spain is operated by IRAM and supported by CNRS (Centre
   National de la Recherche Scientifique, France), MPG
   (MaxPlanck-Gesellschaft, Germany) and IGN (Instituto Geografico
   Nacional, Spain). The SMT is operated by the Arizona Radio Observatory,
   a part of the Steward Observatory of the University of Arizona, with
   financial support of operations from the State of Arizona and financial
   support for instrumentation development from the NSF. The SPT is
   supported by the National Science Foundation through grant PLR-1248097.
   Partial support is also provided by the NSF Physics Frontier Center
   grant PHY-1125897 to the Kavli Institute of Cosmological Physics at the
   University of Chicago, the Kavli Foundation and the Gordon and Betty
   Moore Foundation grant GBMF 947. The SPT hydrogen maser was provided on
   loan from the GLT, courtesy of ASIAA. The EHTC has received generous
   donations of FPGA chips from Xilinx Inc., under the Xilinx University
   Program. The EHTC has benefited from technology shared under open-source
   license by the Collaboration for Astronomy Signal Processing and
   Electronics Research (CASPER). The EHT project is grateful to T4Science
   and Microsemi for their assistance with Hydrogen Masers. This research
   has made use of NASA's Astrophysics Data System. We gratefully
   acknowledge the support provided by the extended staff of the ALMA, both
   from the inception of the ALMA Phasing Project through the observational
   campaigns of 2017 and 2018. We would like to thank A. Deller and W.
   Brisken for EHTspecific support with the use of DiFX. We acknowledge the
   significance that Maunakea, where the SMA and JCMT EHT stations are
   located, has for the indigenous Hawaiian people. The European VLBI
   Network is a joint facility of independent European, African, Asian, and
   North American radio astronomy institutes. Scientific results from data
   presented in this publication are derived from the following EVN project
   code: EH033. This research has made use of data obtained with 12 radio
   telescopes from the East Asian VLBI Network (EAVN): 2 stations from the
   Chinese VLBI Network (the Tianma radio telescope operated by Shanghai
   Astronomical Observatory of Chinese Academy of Sciences (CAS) and the
   Nanshan radio telescope operated by Xinjiang Astronomical Observatory of
   CAS), 2 stations from the Japanese VLBI Network (the Hitachi station
   operated by Ibaraki University and the Kashima station operated by the
   National Institute of Information and Communications Technology), the
   Korean VLBI Network operated by the Korea Astronomy and Space Science
   Institute (KASI), the VLBI Exploration of Radio Astrometry (VERA)
   operated by the National Astronomical Observatory of Japan (NAOJ), and
   the Nobeyama 45m radio telescope operated by NAOJ. We thank VERA staff
   members who helped the operation.; r We are grateful to KVN staff who
   helped to operate the array and to correlate the data for
   quasi-simultaneous multi-wavelength observations of M87. The KVN is a
   facility operated by KASI. The KVN operations are supported by KREONET
   (Korea Research Environment Open NETwork), which is managed and operated
   by KISTI (Korea Institute of Science and Technology Information) The
   VLBA is an instrument of the National Radio Astronomy Observatory. The
   National Radio Astronomy Observatory is a facility of the National
   Science Foundation operated by Associated Universities, Inc. This study
   has been supported in part by the Russian Science Foundation: project
   20-62-46021. The Fermi LAT Collaboration acknowledges generous ongoing
   support from a number of agencies and institutes that have supported
   both the development and the operation of the LAT as well as scientific
   data analysis. These include the National Aeronautics and Space
   Administration and the Department of Energy in the United States, the
   Commissariat a l'Energie Atomique and the Centre National de la
   Recherche Scientifique/Institut National de Physique Nucleaire et de
   Physique des Particules in France, the Agenzia Spaziale Italiana and the
   Istituto Nazionale di Fisica Nucleare in Italy, the Ministry of
   Education, Culture, Sports, Science and Technology (MEXT), High Energy
   Accelerator Research Organization (KEK) and Japan Aerospace Exploration
   Agency (JAXA) in Japan, and the K. A. Wallenberg Foundation, the Swedish
   Research Council and the Swedish National Space Board in Sweden.
   Additional support for science analysis during the operations phase is
   gratefully acknowledged from the Istituto Nazionale di Astrofisica in
   Italy and the Centre National d'Etudes Spatiales in France. This work is
   performed in part under DOE Contract DEAC02-76SF00515. The support of
   the Namibian authorities and of the University of Namibia in
   facilitating the construction and operation of H.E.S.S. is gratefully
   acknowledged, as is the support by the German Ministry for Education and
   Research (BMBF), the Max Planck Society, the German Research Foundation
   (DFG), the Helmholtz Association, the Alexander von Humboldt Foundation,
   the French Ministry of Higher Education, Research and Innovation, the
   Centre National de la Recherche Scientifique (CNRS/IN2P3 and CNRS/INSU),
   the Commissariat a l'energie atomique et aux energies alternatives
   (CEA), the U.K. Science and Technology Facilities Council (STFC), the
   Knut and Alice Wallenberg Foundation, the National Science Centre,
   Poland grant No. 2016/22/M/ST9/00382, the South African Department of
   Science and Technology and National Research Foundation, the University
   of Namibia, the National Commission on Research, Science \&Technology of
   Namibia (NCRST), the Austrian Federal Ministry of Education, Science and
   Research and the Austrian Science Fund (FWF), the Australian Research
   Council (ARC), the Japan Society for the Promotion of Science and by the
   University of Amsterdam. We appreciate the excellent work of the
   technical support staff in Berlin, Zeuthen, Heidelberg, Palaiseau,
   Paris, Saclay, Tubingen, and in Namibia in the construction and
   operation of the equipment. This work benefited from services provided
   by the H.E.S.S. Virtual Organisation, supported by the national resource
   providers of the EGI Federation. We would like to thank the Instituto de
   Astrofisica de Canarias for the excellent working conditions at the
   Observatorio del Roque de los Muchachos in La Palma.; r The financial
   support of the German BMBF, MPG and HGF; the Italian INFN and INAF; the
   Swiss National Fund SNF; the ERDF under the Spanish Ministerio de
   Ciencia e Innovacion (MICINN) (FPA2017-87859-P, FPA2017-85668-P,
   FPA201782729-C6-5-R, FPA2017-90566-REDC, PID2019-104114RBC31,
   PID2019-104114RB-C32, PID2019-105510GB-C31,PID 2019-107847RB-C41,
   PID2019-107847RB-C42, PID2019107988GB-C22); the Indian Department of
   Atomic Energy; the Japanese ICRR, the University of Tokyo, JSPS, and
   MEXT; the Bulgarian Ministry of Education and Science, National RI
   Roadmap Project DO1-268/16.12.2019 and the Academy of Finland grant No.
   320045 is gratefully acknowledged. This work was also supported by the
   Spanish Centro de Excelencia ``Severo Ochoa{''} SEV-2016-0588 and
   CEX2019000920-S, and ``Maria de Maeztu{''} CEX2019-000918-M, the Unidad
   de Excelencia ``Maria de Maeztu{''} MDM-2015-050918-2 and the ``la
   Caixa{''} Foundation (fellowship LCF/BQ/PI18/11630012) and by the CERCA
   program of the Generalitat de Catalunya; by the Croatian Science
   Foundation (HrZZ) Project IP-2016-06-9782 and the University of Rijeka
   Project 13.12.1.3.02; by the DFG Collaborative Research Centers
   SFB823/C4 and SFB876/C3; the Polish National Research Centre grant
   UMO-2016/22/M/ST9/00382; and by the Brazilian MCTIC, CNPq, and FAPERJ.
   This research is supported by grants from the U.S. Department of Energy
   Office of Science, the U.S. National Science Foundation and the
   Smithsonian Institution, by NSERC in Canada, and by the Helmholtz
   Association in Germany. This research used resources provided by the
   Open Science Grid, which is supported by the National Science Foundation
   and the U.S. Department of Energy's Office of Science, and resources of
   the National Energy Research Scientific Computing Center (NERSC), a U.S.
   Department of Energy Office of Science User Facility operated under
   Contract No. DE-AC02-05CH11231. We acknowledge the excellent work of the
   technical support staff at the Fred Lawrence Whipple Observatory and at
   the collaborating institutions in the construction and operation of the
   instrument. Facilities: ALMA, Chandra X-ray Observatory, EAVN, EHT, EVN,
   Fermi, GMVA, H.E.S.S., HSA, HST, KVN, MAGIC, Neil Gehrels Swift
   Observatory, NuSTAR, SMA, VERA, VERITAS, VLBA.},
Number-of-Cited-References = {166},
Times-Cited = {44},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Astrophys. J. Lett.},
Doc-Delivery-Number = {YM9PN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000746900400001},
OA = {Green Submitted, Green Published, hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000359331400003,
Author = {Marrie, Ruth Ann and Bernstein, Charles N. and Peschken, Christine A.
   and Hitchon, Carol A. and Chen, Hui and Fransoo, Randall and Garland,
   Allan},
Title = {Health care utilization before and after intensive care unit admission
   in multiple sclerosis},
Journal = {MULTIPLE SCLEROSIS AND RELATED DISORDERS},
Year = {2015},
Volume = {4},
Number = {4},
Pages = {296-303},
Month = {JUL},
Abstract = {Objectives: The incidence of intensive care unit (ICU) admission is
   elevated in the multiple sclerosis (MS) population but the reasons for
   this are incompletely understood, as are outcomes post-ICU admission.
   Among MS patients we examined the association between ICU admission and
   health care utilization in the year preceding admission, and compared
   health care utilization following ICU admission among persons with MS
   and persons from the general population.
   Methods: We used population-based administrative data from Manitoba,
   Canada to identify 4237 MS cases of which 2547 were incident. We
   compared the incidence rates of ICU admission in the prevalent MS
   population according to health care utilization in the year before
   admission, adjusting for age, sex, comorbidity and socioeconomic status.
   Among incident cases of MS we compared rates of health care utilization
   after ICU admission to those in a matched general population cohort. We
   used generalized linear models adjusting for age, sex, socioeconomic
   status, region, comorbidity and utilization before admission.
   Results: Of 4219 prevalent MS cases, 222 (5.3\%) were admitted to the
   ICU. After adjustment, any hospitalization in the prior year conferred
   an 80\% increased incidence, and physician visits in the highest tertile
   and prescription costs in the highest quartile in the prior year each
   conferred a more than two-fold increased incidence of admission. Among
   2547 incident cases of MS, 109 (4.3\%) were admitted to the ICU and 93
   survived their admission. Thirty-eight percent of the MS population were
   re-hospitalized in the year following admission, similar to the matched
   population (33.8\%). Seven percent of both populations were readmitted
   to the ICU. The MS population had more hospital days after ICU admission
   than the matched population (adjusted RR 3.11; 95\% CI: 1.34-5.90).
   After adjustment the number of physician visits did not differ between
   populations.
   Conclusions: The incidence of ICU admission is higher among persons with
   MS who have higher prior health care utilization. Health care
   utilization remains high after ICU admission. Efforts to prevent ICU
   admission in this population are needed. (C) 2015 The Authors. Published
   by Elsevier B.V. This is an open access article under the CC BY-NC-ND
   license (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Marrie, RA (Corresponding Author), Hlth Sci Ctr, GF-543,820 Sherbrook St, Winnipeg, MB R3A 1R9, Canada.
   Marrie, Ruth Ann; Bernstein, Charles N.; Peschken, Christine A.; Hitchon, Carol A.; Garland, Allan, Univ Manitoba, Dept Internal Med, Winnipeg, MB, Canada.
   Marrie, Ruth Ann; Peschken, Christine A.; Fransoo, Randall; Garland, Allan, Univ Manitoba, Dept Community Hlth Sci, Winnipeg, MB R3T 2N2, Canada.
   Bernstein, Charles N.; Fransoo, Randall, Univ Manitoba, IBD Clin \& Res Ctr, Winnipeg, MB, Canada.
   Chen, Hui; Garland, Allan, Manitoba Ctr Hlth Policy, Winnipeg, MB, Canada.},
DOI = {10.1016/j.msard.2015.05.010},
ISSN = {2211-0348},
EISSN = {2211-0356},
Keywords = {Administrative data; Critical illness; Incidence; Multiple sclerosis;
   Health care utilization},
Keywords-Plus = {QUALITY-OF-LIFE; GLATIRAMER ACETATE; BEHAVIORAL-MODEL; CRITICAL ILLNESS;
   COSTS; SERVICES; DISEASE; MULTICENTER; PREVALENCE; DISABILITY},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Clinical Neurology},
Author-Email = {rmarrie@hsc.mb.ca},
Affiliations = {University of Manitoba; University of Manitoba; University of Manitoba},
ORCID-Numbers = {Marrie, Ruth Ann/0000-0002-1855-5595
   Garland, Allan/0000-0001-7129-936X
   Hitchon, Carol/0000-0001-5547-3268
   Fransoo, Randall/0000-0002-8375-972X},
Funding-Acknowledgement = {Canadian Institutes of Health Research {[}MOP 119318]; Don Paty Career
   Development Award from the MS Society of Canada; Manitoba Centre for
   Health Policy {[}2010-013, 2010/11-15B]},
Funding-Text = {This study was supported (in part) by the Canadian Institutes of Health
   Research (MOP 119318) and a Don Paty Career Development Award from the
   MS Society of Canada. The sponsors had no role in the design and conduct
   of the study; collection, management, analysis, and interpretation of
   the data; and preparation, review, or approval of the manuscript. The
   authors acknowledge the Manitoba Centre for Health Policy for use of the
   Population Health Research Data Repository under project \#2010-013
   (HIPC \#2010/11-15B). The results and conclusions presented are those of
   the authors and no official endorsement by the Manitoba Centre for
   Health Policy, Manitoba Health, or other data providers is intended or
   should be inferred.},
Number-of-Cited-References = {30},
Times-Cited = {11},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Mult. Scler. Relat. Disord.},
Doc-Delivery-Number = {CO7HY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000359331400003},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000467399700004,
Author = {Sandoval, Jorge and Mignot, Emmanuel and Mao, Luca and Pasten, Pablo and
   Bolster, Diogo and Escauriaza, Cristian},
Title = {Field and Numerical Investigation of Transport Mechanisms in a Surface
   Storage Zone},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE},
Year = {2019},
Volume = {124},
Number = {4},
Pages = {938-959},
Month = {APR},
Abstract = {In-stream surface storage zones (SSZs) caused by lateral recirculation
   areas play a significant role in the transport and fate of contaminants
   in rivers. Lateral recirculating areas have long residence times that
   favor nutrient uptake, accumulation of pollutants, and interactions with
   reactive sediments. In watersheds affected by acid-mine drainage, SSZs
   have profound effects on biogeochemical processes, controlling the local
   concentration and distribution of toxic elements along the channel.
   Despite the importance of turbulent flow dynamics on these processes,
   limited work has been carried out to analyze mass transport in natural
   SSZs with complex geometries. In this investigation we study a SSZ in
   the Lluta River, located in a high-altitude environment in northern
   Chile, by coupling field measurements and 3-D numerical simulations to
   understand the transport mechanisms with the main channel. We measure
   the velocity field using an acoustic Doppler velocimeter (ADV) and
   large-scale particle image velocimetry (LSPIV), extracting the
   bathymetry from digital image processing. Using these data, we perform
   detached-eddy simulations (DES) to analyze the mean flow, turbulence
   statistics, and the dynamics of large-scale coherent structures. From
   this detailed description of the turbulent flow, we study the mass
   exchange and the time evolution of the mean concentration of a passive
   scalar in the SSZ by testing three upscaled models: a classical linear
   transport model, a two-storage formulation, and a fractional transport
   model. The analysis integrates temporal and spatial scales to provide a
   new perspective on the turbulent flow in SSZs and their effects on
   global mass transport in rivers.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Escauriaza, C (Corresponding Author), Pontificia Univ Catolica Chile, Dept Ingn Hidraul \& Ambiental, Santiago, Chile.
   Escauriaza, C (Corresponding Author), Ctr Invest Gest Integrada Desastres Nat CIGIDEN, Macul, Chile.
   Sandoval, Jorge; Mignot, Emmanuel; Pasten, Pablo; Escauriaza, Cristian, Pontificia Univ Catolica Chile, Dept Ingn Hidraul \& Ambiental, Santiago, Chile.
   Mignot, Emmanuel, Univ Lyon, CNRS, INSA Lyon, LMFA UMR5509, Villeurbanne, France.
   Mao, Luca, Univ Lincoln, Sch Geog, Lincoln, England.
   Mao, Luca; Escauriaza, Cristian, Ctr Invest Gest Integrada Desastres Nat CIGIDEN, Macul, Chile.
   Pasten, Pablo, Ctr Desarrollo Urbano Sustentable CEDEUS, Providencia, Chile.
   Bolster, Diogo, Univ Notre Dame, Dept Civil \& Environm Engn \& Earth Sci, Notre Dame, IN 46556 USA.},
DOI = {10.1029/2018JF004716},
ISSN = {2169-9003},
EISSN = {2169-9011},
Keywords = {surface storage zones; turbulent coherent structures; detached-eddy
   simulations; transient storage transport models; field measurements},
Keywords-Plus = {SOLUTE TRANSPORT; EXCHANGE PROCESSES; STREAM CONFLUENCE; TRANSIENT
   STORAGE; MASS-EXCHANGE; FLOW; CAVITY; WATER; RIVER; SIMULATION},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {cescauri@ing.puc.cl},
Affiliations = {Pontificia Universidad Catolica de Chile; Centre National de la
   Recherche Scientifique (CNRS); CNRS - Institute for Engineering \&
   Systems Sciences (INSIS); Ecole Centrale de Lyon; Institut National des
   Sciences Appliquees de Lyon - INSA Lyon; Universite Claude Bernard Lyon
   1; Universite Jean Monnet; University of Lincoln; University of Notre
   Dame},
ResearcherID-Numbers = {Mao, Luca/C-6866-2012
   Escauriaza, Cristian/D-6318-2014
   Pastén, Pablo A/D-3604-2014
   Mignot, Emmanuel/F-8180-2011
   Bolster, Diogo/D-9667-2011},
ORCID-Numbers = {Mao, Luca/0000-0001-8619-5221
   Escauriaza, Cristian/0000-0001-5275-8364
   Pastén, Pablo A/0000-0002-9961-9342
   Mignot, Emmanuel/0000-0002-4894-2254
   Bolster, Diogo/0000-0003-3960-4090},
Funding-Acknowledgement = {Fondecyt {[}1130940]; CONICYT/FONDAP {[}15110017]; NLHPC {[}ECM-02]},
Funding-Text = {This work has been supported by Fondecyt grant 1130940. C.E. and L.M.
   acknowledge the funding from CONICYT/FONDAP grant 15110017. This
   research was partially supported by the supercomputing infrastructure of
   the NLHPC (ECM-02). We thank Olivia K. August for motivating the global
   description of mass transport. We greatly appreciate Bruce MacVicar,
   Paul Grams, and two anonymous reviewers for their contributions to
   improve the quality of this paper. The data from field measurements is
   available for download in the following open data repository
   (https://doi.org/10.5281/zenodo.1345310).},
Number-of-Cited-References = {61},
Times-Cited = {20},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {17},
Journal-ISO = {J. Geophys. Res.-Earth Surf.},
Doc-Delivery-Number = {HX4VV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000467399700004},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000853540600001,
Author = {Cai, Yangyang and Lv, Dezhong and Li, Donghao and Yin, Jiaqi and Ma,
   Yingying and Luo, Ya and Fu, Limei and Ding, Na and Li, Yongsheng and
   Pan, Zhenwei and Li, Xia and Xu, Juan},
Title = {IEAtlas: an atlas of HLA-presented immune epitopes derived from
   non-coding regions},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2023},
Volume = {51},
Number = {D1},
Pages = {D409-D417},
Month = {JAN 6},
Abstract = {Cancer-related epitopes can engage the immune system against tumor
   cells, thus exploring epitopes derived from non-coding regions is
   emerging as a fascinating field in cancer immunotherapies. Here, we
   described a database, IEAtlas (), which aims to provide and visualize
   the comprehensive atlas of human leukocyte antigen (HLA)-presented
   immunogenic epitopes derived from non-coding regions. IEAtlas reanalyzed
   publicly available mass spectrometry-based HLA immunopeptidome datasets
   against our integrated benchmarked non-canonical open reading frame
   information. The current IEAtlas identified 245 870 non-canonical
   epitopes binding to HLA-I/II allotypes across 15 cancer types and 30
   non-cancerous tissues, greatly expanding the cancer immunopeptidome.
   IEAtlas further evaluates the immunogenicity via several commonly used
   immunogenic features, including HLA binding affinity, stability and
   T-cell receptor recognition. In addition, IEAtlas provides the
   biochemical properties of epitopes as well as the clinical relevance of
   corresponding genes across major cancer types and normal tissues.
   Several flexible tools were also developed to aid retrieval and to
   analyze the epitopes derived from non-coding regions. Overall, IEAtlas
   will serve as a valuable resource for investigating the immunogenic
   capacity of non-canonical epitopes and the potential as therapeutic
   cancer vaccines.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Li, X; Xu, J (Corresponding Author), Harbin Med Univ, Coll Bioinformat Sci \& Technol, Harbin 150081, Heilongjiang, Peoples R China.
   Li, YS; Li, X (Corresponding Author), Hainan Med Univ, Key Lab Trop Translat Med, Minist Educ, Coll Biomed Informat \& Engn,Hainan Women \& Childr, Haikou 571199, Hainan, Peoples R China.
   Pan, ZW (Corresponding Author), Harbin Med Univ, Dept Pharmacol, State Prov Key Labs Biomed Pharmaceut China, Key Lab Cardiovasc Res,Minist Educ,Coll Pharm, Harbin 150086, Heilongjiang, Peoples R China.
   Pan, ZW (Corresponding Author), Harbin Med Univ, NHC Key Lab Cell Transplantat, Affiliated Hosp 1, Harbin 150001, Heilongjiang, Peoples R China.
   Cai, Yangyang; Lv, Dezhong; Li, Donghao; Yin, Jiaqi; Ma, Yingying; Luo, Ya; Fu, Limei; Ding, Na; Li, Xia; Xu, Juan, Harbin Med Univ, Coll Bioinformat Sci \& Technol, Harbin 150081, Heilongjiang, Peoples R China.
   Li, Yongsheng; Li, Xia, Hainan Med Univ, Key Lab Trop Translat Med, Minist Educ, Coll Biomed Informat \& Engn,Hainan Women \& Childr, Haikou 571199, Hainan, Peoples R China.
   Pan, Zhenwei, Harbin Med Univ, Dept Pharmacol, State Prov Key Labs Biomed Pharmaceut China, Key Lab Cardiovasc Res,Minist Educ,Coll Pharm, Harbin 150086, Heilongjiang, Peoples R China.
   Pan, Zhenwei, Harbin Med Univ, NHC Key Lab Cell Transplantat, Affiliated Hosp 1, Harbin 150001, Heilongjiang, Peoples R China.},
DOI = {10.1093/nar/gkac776},
EarlyAccessDate = {SEP 2022},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {MASS-SPECTROMETRY; DATA REPOSITORY; TUMOR; IDENTIFICATION; PREDICTION},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {liyongsheng@hainmc.edu.cn
   panzw@ems.hrbmu.edu.cn
   lixia@hrbmu.edu.cn
   xujuanbiocc@ems.hrbmu.edu.cn},
Affiliations = {Harbin Medical University; Hainan Medical University; Harbin Medical
   University; Harbin Medical University},
ResearcherID-Numbers = {Zhang, Xiaofeng/JMC-6060-2023
   Cheng, Yuan/JKJ-0794-2023
   xu, lingzhi/JVZ-8748-2024
   Liu, Yixuan/JFJ-2820-2023
   Wang, Jiacheng/ABE-5948-2020
   li, xia/HHZ-7468-2022
   WU, ZHEN/GRN-7688-2022
   Ma, Ying/HKN-2215-2023
   Zhang, Yihao/JGM-3514-2023
   },
ORCID-Numbers = {Zhang, Xiaofeng/0000-0003-2738-3286
   WU, ZHEN/0000-0001-8719-057X
   Li, Yongsheng/0000-0001-6047-9592},
Funding-Acknowledgement = {National Natural Science Foundation of China {[}32170676, 31871338,
   31970646, 32060152, 32070673]; Natural Science Foundation for
   Distinguished Young Scholars of Heilongjiang Province {[}JQ2019C004];
   HMU Marshal Initiative Funding {[}HMUMIF-21024, HMUMIF-21017]; Marshal
   Initiative Funding of Hainan Medical University {[}JBGS202103]; Hainan
   Province Science and Technology Special Fund {[}ZDYF2021SHFZ051]; Hainan
   Provincial Natural Science Foundation of China {[}820MS053]; Major
   Science and Technology Program of Hainan Province {[}ZDKJ202003];
   National Key R\&D Program of China {[}2018YFC2000100]; Bioinformatics
   for Mjaor Diseases Science Innovation Group of Hainan Medical
   University; Heilongjiang Touyan Innovation Team Program},
Funding-Text = {This work was supported by the National Natural Science Foundation of
   China {[}32170676, 31871338, 31970646, 32060152 and 32070673]; Natural
   Science Foundation for Distinguished Young Scholars of Heilongjiang
   Province {[}JQ2019C004]; HMU Marshal Initiative Funding {[}HMUMIF-21024
   and HMUMIF-21017]; Marshal Initiative Funding of Hainan Medical
   University {[}JBGS202103]; Hainan Province Science and Technology
   Special Fund {[}ZDYF2021SHFZ051]; Hainan Provincial Natural Science
   Foundation of China {[}820MS053]; Major Science and Technology Program
   of Hainan Province {[}ZDKJ202003]; the National Key R\&D Program of
   China {[}2018YFC2000100]; Bioinformatics for Mjaor Diseases Science
   Innovation Group of Hainan Medical University and Heilongjiang Touyan
   Innovation Team Program. Funding for open access charge: National
   Natural Science Foundation of China.},
Number-of-Cited-References = {46},
Times-Cited = {8},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {12},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {Q5NY7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000853540600001},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000298601300044,
Author = {Letunic, Ivica and Doerks, Tobias and Bork, Peer},
Title = {SMART 7: recent updates to the protein domain annotation resource},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2012},
Volume = {40},
Number = {D1},
Pages = {D302-D305},
Month = {JAN},
Abstract = {SMART (Simple Modular Architecture Research Tool) for the identification
   and annotation of protein domains and the analysis of protein domain
   architectures. SMART version 7 contains manually curated models for 1009
   protein domains, 200 more than in the previous version. The current
   release introduces several novel features and a streamlined user
   interface resulting in a faster and more comfortable workflow. The
   underlying protein databases were greatly expanded, resulting in a
   2-fold increase in number of annotated domains and features. The
   database of completely sequenced genomes now includes 1133 species,
   compared to 630 in the previous release. Domain architecture analysis
   results can now be exported and visualized through the iTOL phylogenetic
   tree viewer. `metaSMART' was introduced as a novel subresource dedicated
   to the exploration and analysis of domain architectures in various
   metagenomics data sets. An advanced full text search engine was
   implemented, covering the complete annotations for SMART and Pfam
   domains, as well as the complete set of protein descriptions, allowing
   users to quickly find relevant information.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Bork, P (Corresponding Author), European Mol Biol Lab, Meyerhofstr 1, D-69012 Heidelberg, Germany.
   Letunic, Ivica; Doerks, Tobias; Bork, Peer, European Mol Biol Lab, D-69012 Heidelberg, Germany.},
DOI = {10.1093/nar/gkr931},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {INTERACTIVE TREE; DISPLAY; GENOMES; TOOL},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {bork@embl.de},
Affiliations = {European Molecular Biology Laboratory (EMBL)},
ResearcherID-Numbers = {Letunic, Ivica/K-1102-2019
   Bork, Peer/F-1813-2013
   Letunic, Ivica/A-6032-2009},
ORCID-Numbers = {Letunic, Ivica/0000-0003-3560-4288
   Bork, Peer/0000-0002-2627-833X
   },
Funding-Acknowledgement = {EMBL; European Union {[}213037]},
Funding-Text = {EMBL (internal budget) and the European Union under the program `FP7
   capacities: Scientific Data Repositories' (grant 213037) (IMproving
   Protein Annotation and Co-ordination using Technology - IMPACT). Funding
   for open access charge: EMBL (internal budget).},
Number-of-Cited-References = {19},
Times-Cited = {458},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {14},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {869MD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000298601300044},
OA = {gold, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000923535000001,
Author = {Weigard, Alexander and Matzke, Dora and Tanis, Charlotte and Heathcote,
   Andrew},
Title = {A cognitive process modeling framework for the ABCD study stop-signal
   task},
Journal = {DEVELOPMENTAL COGNITIVE NEUROSCIENCE},
Year = {2023},
Volume = {59},
Month = {FEB},
Abstract = {The Adolescent Brain Cognitive Development (ABCD) Study is a
   longitudinal neuroimaging study of unprece-dented scale that is in the
   process of following over 11,000 youth from middle childhood though age
   20. However, a design feature of the study's stop-signal task violates
   ``context independence{''}, an assumption critical to current
   non-parametric methods for estimating stop-signal reaction time (SSRT),
   a key measure of inhibitory ability in the study. This has led some
   experts to call for the task to be changed and for previously collected
   data to be used with caution. We present a cognitive process modeling
   framework, the RDEX-ABCD model, that provides a parsimonious explanation
   for the impact of this design feature on ``go{''} stimulus processing
   and successfully accounts for key behavioral trends in the ABCD data.
   Simulation studies using this model suggest that failing to account for
   the context independence violations in the ABCD design can lead to
   erroneous in-ferences in several realistic scenarios. However, we
   demonstrate that RDEX-ABCD effectively addresses these violations and
   can be used to accurately measure SSRT along with an array of additional
   mechanistic parameters of interest (e.g., attention to the stop signal,
   cognitive efficiency), advancing investigators' ability to draw valid
   and nuanced inferences from ABCD data.Availability of data and
   materials: Data from the ABCD Study are available through the NIH Data
   Archive (NDA): nda.nih.gov/abcd. Code for all analyses featured in this
   study is openly available on the Open Science Framework (OSF):
   osf.io/2h8a7/.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Weigard, A (Corresponding Author), Univ Michigan, Dept Psychiat, Rachel Upjohn Bldg,4250 Plymouth Rd, Ann Arbor, MI 48109 USA.
   Weigard, Alexander, Univ Michigan, Dept Psychiat, Ann Arbor, MI USA.
   Matzke, Dora; Tanis, Charlotte; Heathcote, Andrew, Univ Amsterdam, Dept Psychol, Amsterdam, Netherlands.
   Heathcote, Andrew, Univ Newcastle, Sch Psychol, Callaghan, Australia.
   Weigard, Alexander, Univ Michigan, Dept Psychiat, Rachel Upjohn Bldg,4250 Plymouth Rd, Ann Arbor, MI 48109 USA.},
DOI = {10.1016/j.dcn.2022.101191},
EarlyAccessDate = {JAN 2023},
Article-Number = {101191},
ISSN = {1878-9293},
EISSN = {1878-9307},
Keywords = {Inhibition; Evidence accumulation; Trigger failure; Bayesian cognitive
   modeling; Parameter recovery},
Keywords-Plus = {RESPONSE-INHIBITION; DECISION-MAKING; ATTENTION; FAILURES; ABILITY; ACT;
   PSYCHOPATHOLOGY; DISTRIBUTIONS; ADOLESCENTS; RELIABILITY},
Research-Areas = {Psychology; Neurosciences \& Neurology},
Web-of-Science-Categories  = {Psychology, Developmental; Neurosciences},
Author-Email = {asweigar@med.umich.edu},
Affiliations = {University of Michigan System; University of Michigan; University of
   Amsterdam; University of Newcastle; University of Michigan System;
   University of Michigan},
ResearcherID-Numbers = {Heathcote, Andrew/C-1856-2008
   },
ORCID-Numbers = {Heathcote, Andrew/0000-0003-4324-5537
   Tanis, Charlotte/0000-0003-3466-4414},
Funding-Acknowledgement = {National Institute on Alcohol Abuse Alcoholism {[}T32 AA007477];
   National Institute on Drug Abuse {[}K23 DA051561]; Vidi grant from
   Netherlands Organization for Scientific Research (NWO)
   {[}VI.Vidi.191.091]; Advanced ERC grant {[}743086]; UNIFY {[}743086];
   Australian Research Council {[}DP210100313, DP200100655]; Revesz
   Visiting Professor Fellowship at Department of Psychology, University of
   Amsterdam; National Institutes of Health {[}U01DA041048, U01DA050989,
   U01DA051016, U01DA041022, U01DA051018, U01DA051037, U01DA050987,
   U01DA041174, U01DA041106, U01DA041117, U01DA041028, U01DA041134,
   U01DA050988, U01DA051039, U01DA041156, U01DA041025, U01DA041120,
   U01DA051038, U01DA041148, U01DA041093, U01DA041089, U24DA041123,
   U24DA041147]; European Research Council (ERC) {[}743086] Funding Source:
   European Research Council (ERC); Australian Research Council
   {[}DP200100655] Funding Source: Australian Research Council},
Funding-Text = {A.W. was supported by National Institute on Alcohol Abuse \& Alcoholism
   T32 AA007477 (to Frederic Blow) and National Institute on Drug Abuse K23
   DA051561.DM was supported by a Vidi grant (VI.Vidi.191.091) from the
   Netherlands Organization for Scientific Research (NWO). C.T. was
   supported by an Advanced ERC grant 743086 UNIFY (to Eric-Jan
   Wagenmakers). A.H. was supported by 743086 UNIFY, Australian Research
   Council grants DP210100313 and DP200100655, and a Revesz Visiting
   Professor Fellowship at the Department of Psychology, University of
   Amsterdam.Data used in the preparation of this article were obtained
   from the Adolescent Brain Cognitive Development<SUP>SM</SUP> (ABCD)
   Study (https:// abcdstudy.org), held in the NIMH Data Archive (NDA).
   This is a multisite, longitudinal study designed to recruit more than
   10,000 children age 9-10 and follow them over 10 years into early
   adulthood. The ABCD Study (R) is supported by the National Institutes of
   Health and additional federal partners under award numbers U01DA041048,
   U01DA050989, U01DA051016, U01DA041022, U01DA051018, U01DA051037,
   U01DA050987, U01DA041174, U01DA041106, U01DA041117, U01DA041028,
   U01DA041134, U01DA050988, U01DA051039, U01DA041156, U01DA041025,
   U01DA041120, U01DA051038, U01DA041148, U01DA041093, U01DA041089,
   U24DA041123, U24DA041147. A full list of supporters is available at
   https://abcdstudy. org/federal-partners.html. A listing of participating
   sites and a complete listing of the study investigators can be found at
   https://abcdstudy.org/consortium\_members/. ABCD consortium
   investigators designed and implemented the study and/or provided data
   but did not necessarily participate in analysis or writing of this
   report. This manuscript reflects the views of the authors and may not
   reflect the opinions or views of the NIH or ABCD consortium
   investigators. The ABCD data repository grows and changes over time. The
   ABCD data used in this report came from ABCD Release 1.1, DOI
   10.15154/1412097.},
Number-of-Cited-References = {75},
Times-Cited = {0},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {3},
Journal-ISO = {Dev. Cogn. Neurosci.},
Doc-Delivery-Number = {8L1FP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000923535000001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:001102636000001,
Author = {Maukel, Lisa-Marie and Weidner, Gerdi and Beyersmann, Jan and Spaderna,
   Heike},
Title = {Adverse events after left ventricular assist device implantation linked
   to psychosocial risk in women and men},
Journal = {JOURNAL OF HEART AND LUNG TRANSPLANTATION},
Year = {2023},
Volume = {42},
Number = {11},
Pages = {1557-1568},
Month = {NOV},
Abstract = {BACKGROUND: Reasons for women's increased probability to experience
   adverse events (AEs) after left ventricular assist device (LVAD)
   implantation compared with men's remain uncertain. We explored the role
   of psychosocial risk in the experience of AEs in women and men.METHODS:
   INTERMACS patients receiving a primary continuous-flow LVAD between July
   2006 and December 2017, median follow-up 13.6 months, were included (n =
   20,123, 21.3\% women). Time-to-event was calculated with cumulative
   incidence functions for 10 types of AEs separately (e.g., infection,
   device malfunction), each time accounting for the competing outcomes
   death, heart transplant, and device explant due to recovery.
   Event-specific Cox proportional hazard models were run with a binary
   psychosocial risk variable (including substance abuse, psychiatric
   diagnosis, limited social support, limited cognition, repeated
   noncompliance), controlled for covariates. RESULTS: Psychosocial risk
   was more prevalent in men than in women (21.4\% vs 17.5\%, p < 0.001).
   Seven out of 10 AEs were more likely in women than in men (e.g.,
   infection 44.5\% vs 39.2\%, p < 0.001). The association of psychosocial
   risk with each AE was either stronger in women than in men (e.g., device
   malfunction HRadj 1.29, 95\% confidence interval (CI) (1.06-1.56) vs
   HRadj 1.10, 95\% CI (0.97-1.25); rehospitalization HRadj 1.15, 95\% CI
   (1.02-1.29) vs HRadj 1.03, 95\% CI (0.97-1.10) or similar between
   sexes.CONCLUSIONS: Independent of clinical parameters, the presence of
   psychosocial risk is associated with increases in AEs. This suggests
   that early modification of psychosocial risk factors may have the
   potential to lower the risk for AEs in this patient population.(c) 2023
   The Authors. Published by Elsevier Inc. on behalf of International
   Society for Heart and Lung Transplantation. All rights reserved. This is
   an open access article under the CC BY-NC-ND license
   (http://creativecommons.org/licenses/by-nc-nd/4.0/).},
Publisher = {ELSEVIER SCIENCE INC},
Address = {STE 800, 230 PARK AVE, NEW YORK, NY 10169 USA},
Type = {Article},
Language = {English},
Affiliation = {Spaderna, H (Corresponding Author), Trier Univ, Fac 1, Sect Hlth Psychol, Nursing Sci, Univ Ring 15, D-54296 Trier, Germany.
   Maukel, Lisa-Marie; Spaderna, Heike, Trier Univ, Sect Hlth Psychol, Nursing Sci, Trier, Germany.
   Weidner, Gerdi, San Francisco State Univ, Biol, San Francisco, CA USA.
   Beyersmann, Jan, Ulm Univ, Inst Stat, Ulm, Germany.
   Spaderna, Heike, Trier Univ, Fac 1, Sect Hlth Psychol, Nursing Sci, Univ Ring 15, D-54296 Trier, Germany.},
DOI = {10.1016/j.healun.2023.06.013},
ISSN = {1053-2498},
EISSN = {1557-3117},
Keywords = {left ventricular assist device; adverse events; sex differences;
   psychosocial risk},
Keywords-Plus = {MECHANICAL CIRCULATORY SUPPORT; SEX-DIFFERENCES; GENDER-DIFFERENCES;
   HEART-FAILURE; OUTCOMES; REGISTRY; SOCIETY; STROKE; TESTS},
Research-Areas = {Cardiovascular System \& Cardiology; Respiratory System; Surgery;
   Transplantation},
Web-of-Science-Categories  = {Cardiac \& Cardiovascular Systems; Respiratory System; Surgery;
   Transplantation},
Author-Email = {spaderna@uni-trier.de},
Affiliations = {Universitat Trier; California State University System; San Francisco
   State University; Ulm University; Universitat Trier},
ResearcherID-Numbers = {Maukel, Lisa-Marie/HHC-3062-2022},
ORCID-Numbers = {Maukel, Lisa-Marie/0000-0002-3493-1378},
Funding-Acknowledgement = {German Research Foundation {[}SP945/2-1]; Alexander von Humboldt
   Foundation {[}USA/1071425]; Trier University},
Funding-Text = {None of the authors has a financial relationship with a commercial
   entity that has an interest in the subject of the presented manuscript
   or other conflicts of interest to dis -close. This manuscript was
   prepared using INTERMACS Research Materials obtained from the NHLBI
   Biologic Specimen and Data Repository Information Coordinating Center
   and does not necessarily reflect the opinions or views of INTERMACS or
   the NHLBI. The authors thank all clinicians who contributed data to the
   INTERMACS database, and the reviewers for their comments and
   suggestions, which helped to improve this manuscript. This work was
   supported by grants from the German Research Foundation (HS, GW;
   SP945/2-1), the Alexander von Humboldt Foundation (GW, HS, USA/1071425),
   and Trier University. Part of this work was presented at the
   International Scientific Workshop ``The Relevance of Registry Research
   for Clinical Practice: Gender Differences in Left Ventricular Assist
   Device Recipients with a Focus on Psychosocial and Behavioral
   Factors{''}, Trier, Germany, October 10-12, 2019; the 42nd Annual
   Meeting of the International Society for Heart and Lung Transplantation,
   Boston, MA, April 27-30, 2022; and at the 52nd Congress of the German
   Psychological Society (Deutsche Gesellschaft fur Psychologie, DGPs),
   Hildesheim, Germany, September 10-15, 2022.},
Number-of-Cited-References = {40},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {J. Heart Lung Transplant.},
Doc-Delivery-Number = {Y0ZL1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001102636000001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000529107400004,
Author = {Helanow, Christian and Iverson, Neal R. and Zoet, Lucas K. and
   Gagliardini, Olivier},
Title = {Sliding Relations for Glacier Slip With Cavities Over Three-Dimensional
   Beds},
Journal = {GEOPHYSICAL RESEARCH LETTERS},
Year = {2020},
Volume = {47},
Number = {3},
Month = {FEB 16},
Abstract = {Results of glacier flow models and associated estimates of future sea
   level rise depend sensitively on the prescribed relation between shear
   stress and slip velocity at the glacier bed. Using a fully
   three-dimensional numerical model of ice flow, we compute steady-state
   sliding relations for where ice slips over a rock bed with
   three-dimensional, periodic topography. In agreement with studies of
   two-dimensional beds, water-filled cavities that form down-glacier from
   bedforms cause basal shear stress to peak at a threshold slip velocity
   and decrease at higher velocities (i.e., rate-weakening drag). However,
   the shear stress magnitude and extent of rate-weakening drag depend
   systematically on lateral topographic variations not considered
   previously. Moreover, steep up-glacier-facing slopes of bedforms can
   result in shear stress that increases monotonically over a wide range of
   slip velocity, helping to stabilize slip. These results highlight the
   potential variability of sliding relations and their likely sensitivity
   to the morphological diversity of glacier beds.
   Plain Language Summary Parts of ice sheets that flow into the oceans and
   affect sea level can flow unusually fast by slipping over their beds. We
   use a computer to solve for the first time in three dimensions the
   equations that describe the flow of ice as it slips over a bumpy rock
   bed. We include the important tendency for glaciers to separate from
   rock and form water-filled cavities down-glacier from bumps. These
   calculations indicate that resistance to slip depends sensitively on the
   bump shape and spacing. Cavities can cause the bed to become more
   slippery the faster the ice slides, with this destabilizing effect being
   more severe for bumps that are laterally narrow and widely spaced.
   However, bumps with steeply sloping up-glacier sides can reverse this
   effect and cause resistance to slip to increase over a wide range of
   increasing slip velocity. This diverse behavior highlights the need for
   estimates of glacier slip velocity to incorporate the actual topography
   of glacier beds.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Helanow, C (Corresponding Author), Iowa State Univ, Dept Geol \& Atmospher Sci, Ames, IA 50011 USA.
   Helanow, Christian; Iverson, Neal R., Iowa State Univ, Dept Geol \& Atmospher Sci, Ames, IA 50011 USA.
   Zoet, Lucas K., Univ Wisconsin, Dept Geosci, Madison, WI USA.
   Gagliardini, Olivier, Univ Grenoble Alpes, IGE, CNRS, IRD, Grenoble, France.},
DOI = {10.1029/2019GL084924},
Article-Number = {e2019GL084924},
ISSN = {0094-8276},
EISSN = {1944-8007},
Keywords-Plus = {SUBGLACIAL WATER-PRESSURE; SEA-LEVEL; ICE; FRICTION; MECHANISM;
   PATTERNS; VELOCITY; EROSION},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {helanow@iastate.edu},
Affiliations = {Iowa State University; University of Wisconsin System; University of
   Wisconsin Madison; Centre National de la Recherche Scientifique (CNRS);
   Institut de Recherche pour le Developpement (IRD); Communaute Universite
   Grenoble Alpes; Universite Grenoble Alpes (UGA)},
ResearcherID-Numbers = {Gagliardini, Olivier/GQQ-1222-2022
   },
ORCID-Numbers = {Gagliardini, Olivier/0000-0001-9162-3518
   Zoet, Lucas/0000-0002-9635-4051},
Funding-Acknowledgement = {U.S. National Science Foundation {[}EAR-1660972]; French National
   Research Agency project SAUSSURE {[}ANR-18-CE01-0015-01]; Agence
   Nationale de la Recherche (ANR) {[}ANR-18-CE01-0015] Funding Source:
   Agence Nationale de la Recherche (ANR)},
Funding-Text = {Contributions to this work by C. H., N. I., and L. Z. were supported by
   a grant from the U.S. National Science Foundation (EAR-1660972) to N. I
   and L. Z. O. G. was supported by the French National Research Agency
   project SAUSSURE (ANR-18-CE01-0015-01). Functions specifying the bed
   topographies and numerical values for the variables used in the sliding
   relations are permanently archived at the Iowa State University Open
   Data repository (https://doi.org/10.25380/iastate.11354111).We
   appreciate the constructive comments by V. Tsai and two anonymous
   reviewers on an earlier version of the manuscript.},
Number-of-Cited-References = {53},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Geophys. Res. Lett.},
Doc-Delivery-Number = {LH9MN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000529107400004},
OA = {Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000529516200001,
Author = {Mao, Luca and Toro, Matteo and Carrillo, Ricardo and Brardinoni,
   Francesco and Fraccarollo, Luigi},
Title = {Controls Over Particle Motion and Resting Times of Coarse Bed Load
   Transport in a Glacier-Fed Mountain Stream},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE},
Year = {2020},
Volume = {125},
Number = {4},
Month = {APR},
Abstract = {Coarse bed load transport is a crucial process in river morphodynamics
   but is difficult to monitor in mountain streams. Here we present a new
   sediment transport data set obtained from 2 years of field-based
   monitoring (2014-2015) at the Estero Morales, a high-gradient stream in
   the central Chilean Andes. This stream features step-pool bed geometry
   and a glacier-fed hydrologic regime characterized by abrupt daily
   fluctuations in discharge. Bed load was monitored directly using Bunte
   samplers and by surveying the mobility of passive integrated transponder
   (PIT) tags. We used the competence method to quantify the effective
   slope, which is the fraction of the topographical slope responsible for
   bed load transport. This accounts for only 10\% of the topographical
   slope, confirming that most of the energy is dissipated on
   macroroughness elements. We used the displacement lengths of PIT tags to
   analyze displacement lengths and virtual velocity of a wide range of
   tracer sizes (38-415 mm). Bed load transport in the Estero Morales shown
   to be size-selective, and the distance between steps influences the
   displacement lengths of PIT tags. Displacement lengths were also used to
   derive the statistics of flight distances and resting times. Our results
   show that the average length of flight scales inversely to grain size.
   This contradicts Einstein's conjecture about the linear relationship
   between grain size and intervals between resting periods in a steep
   step-pool stream in ordinary flood conditions.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Mao, L (Corresponding Author), Univ Lincoln, Sch Geog, Lincoln, England.
   Mao, L (Corresponding Author), Pontificia Univ Catolica Chile, Inst Geog, Santiago, Chile.
   Mao, Luca, Univ Lincoln, Sch Geog, Lincoln, England.
   Mao, Luca, Pontificia Univ Catolica Chile, Inst Geog, Santiago, Chile.
   Toro, Matteo; Fraccarollo, Luigi, Univ Trento, Dept Civil Environm \& Mech Engn, Trento, Italy.
   Carrillo, Ricardo, Pontificia Univ CatOlica Chile, Dept Ecosyst \& Environm, Santiago, Chile.
   Brardinoni, Francesco, Univ Bologna, Dept Biol Geol \& Environm Sci, Bologna, Italy.},
DOI = {10.1029/2019JF005253},
Article-Number = {e2019JF005253},
ISSN = {2169-9003},
EISSN = {2169-9011},
Keywords-Plus = {BEDLOAD TRANSPORT; SEDIMENT TRANSPORT; VIRTUAL VELOCITY; GRAVEL; RIVER;
   ENTRAINMENT; CHANNEL; SIZE; CALIBRATION; MORPHOLOGY},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {lumao@lincoln.ac.uk},
Affiliations = {University of Lincoln; Pontificia Universidad Catolica de Chile;
   University of Trento; Pontificia Universidad Catolica de Chile;
   University of Bologna},
ResearcherID-Numbers = {Brardinoni, Francesco/IAS-0015-2023
   Mao, Luca/C-6866-2012
   },
ORCID-Numbers = {Mao, Luca/0000-0001-8619-5221
   Fraccarollo, Luigi/0000-0003-2512-1549
   matteo, toro/0000-0002-9939-8607
   BRARDINONI, FRANCESCO/0000-0002-3525-3599
   Carrillo Munoz, Ricardo/0000-0001-5110-6268},
Funding-Acknowledgement = {project Fondecyt Regular {[}1170657]},
Funding-Text = {This work was supported by the project Fondecyt Regular (1170657). We
   thank Joaquin Lobato, Juan Pablo del Pedregal, Enzo Montenegro, Paolo
   Bertoncello, and Riccardo Rainato for their help in the field. We are
   grateful to the Chilean National Park Service (CONAF) for providing
   access to the sample locations and on-site support of our research. Two
   anonymous reviewers, John Laronne, and the Associate Editor Luca Solari
   are thanked for providing several constructive commentaries on a first
   version of the manuscript. The data from field measurements are
   available for download in an online open data repository (DOI:
   10.5281/zenodo.3274762).},
Number-of-Cited-References = {78},
Times-Cited = {6},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {10},
Journal-ISO = {J. Geophys. Res.-Earth Surf.},
Doc-Delivery-Number = {LI5HF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000529516200001},
OA = {Green Accepted, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000300727500001,
Author = {Burge, Sarah and Kelly, Elizabeth and Lonsdale, David and
   Mutowo-Muellenet, Prudence and McAnulla, Craig and Mitchell, Alex and
   Sangrador-Vegas, Amaia and Yong, Siew-Yit and Mulder, Nicola and Hunter,
   Sarah},
Title = {Manual GO annotation of predictive protein signatures: the InterPro
   approach to GO curation},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2012},
Month = {FEB 1},
Abstract = {InterPro amalgamates predictive protein signatures from a number of
   well-known partner databases into a single resource. To aid with
   interpretation of results, InterPro entries are manually annotated with
   terms from the Gene Ontology (GO). The InterPro2GO mappings are
   comprised of the cross-references between these two resources and are
   the largest source of GO annotation predictions for proteins. Here, we
   describe the protocol by which InterPro curators integrate GO terms into
   the InterPro database. We discuss the unique challenges involved in
   integrating specific GO terms with entries that may describe a diverse
   set of proteins, and we illustrate, with examples, how InterPro
   hierarchies reflect GO terms of increasing specificity. We describe a
   revised protocol for GO mapping that enables us to assign GO terms to
   domains based on the function of the individual domain, rather than the
   function of the families in which the domain is found. We also discuss
   how taxonomic constraints are dealt with and those cases where we are
   unable to add any appropriate GO terms. Expert manual annotation of
   InterPro entries with GO terms enables users to infer function, process
   or subcellular information for uncharacterized sequences based on
   sequence matches to predictive models.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Hunter, S (Corresponding Author), EMBL EBI, Wellcome Trust Genome Campus, Hinxton CB10 1SD, Cambs, England.
   Burge, Sarah; Lonsdale, David; Mutowo-Muellenet, Prudence; McAnulla, Craig; Mitchell, Alex; Sangrador-Vegas, Amaia; Yong, Siew-Yit; Hunter, Sarah, EMBL EBI, Hinxton CB10 1SD, Cambs, England.
   Kelly, Elizabeth; Mulder, Nicola, Univ Cape Town, Dept Clin Lab Sci, Inst Infect Dis \& Mol Med, Computat Biol Grp,Med Sch, ZA-7925 Cape Town, South Africa.},
DOI = {10.1093/database/bar068},
Article-Number = {bar068},
ISSN = {1758-0463},
Keywords-Plus = {GENE ONTOLOGY; DATABASE; DOMAINS; FAMILY; SETS},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {hunter@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL); University of Cape Town},
ResearcherID-Numbers = {Mulder, Nicola J/JFS-0309-2023
   },
ORCID-Numbers = {Mulder, Nicola J/0000-0003-4905-0941
   Yong, Siew Yit/0000-0002-1952-3528
   Burge, Sarah/0000-0002-2506-927X
   Mutowo, Prudence/0000-0002-4646-4172
   Hunter, Sarah/0000-0003-2453-0770
   Sangrador, Amaia/0000-0001-6688-429X
   Mitchell, Alex/0000-0001-8655-7966},
Funding-Acknowledgement = {European Union {[}213037]; EMBL; BBSRC {[}BB/F010508/1]; BBSRC
   {[}BB/F010508/1] Funding Source: UKRI; Biotechnology and Biological
   Sciences Research Council {[}BB/F010508/1] Funding Source: researchfish},
Funding-Text = {European Union under the program `FP7 capacities: Scientific Data
   Repositories' (grant number 213037). The project is entitled IMproving
   Protein Annotation and Co-ordination using Technology (IMPACT). BBSRC
   Bioinformatics and Biological Resources Fund (grant BB/F010508/1).
   Funding for open access charge: EMBL.},
Number-of-Cited-References = {15},
Times-Cited = {51},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {Database},
Doc-Delivery-Number = {898GN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000300727500001},
OA = {Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001039846900001,
Author = {Priesmeier, Laura and Schoger, Eric and Cyganek, Lukas and Zelarayan,
   Laura Cecilia},
Title = {Single Combining a tetracycline (Tet)-inducible gRNA system and CRISPRa
   for titratable and timely controlled enhancement of endogenous<i>
   SHISA3</i> activation in human induced pluripotent stem cells (hiPSC)},
Journal = {STEM CELL RESEARCH},
Year = {2023},
Volume = {71},
Month = {SEP},
Abstract = {Towards increasing the possibility for temporal control of gene
   expression using CRISPR activation (a) systems, we generated homozygous
   human induced pluripotent stem cell (hiPSC) lines carrying a doxycycline
   (dox)-inducible guide(g)-RNA construct targeting the SHISA3
   transciptional start site, as proof-of-principle, or a non targeting
   gRNA as a control. The dox-inducible gRNA cassette was inserted into the
   human ROSA26 locus in a line with dCas9VPR integrated at the AAVS1 locus
   (CRISPRa/Tet-iSHISA3). Pluripotency, genomic integrity and
   differentiation potential into all three germ layers were maintained.
   Dox-dependent gene induction was validated in hiPSCs as well as derived
   fibroblasts. These lines provide an attractive tool for cellular
   reprogramming in hiPSC-derived cells in a timely controlled manner.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Zelarayán, LC (Corresponding Author), Univ Med Ctr Goettingen UMG, Inst Pharmacol \& Toxicol, D-37075 Gottingen, Germany.
   Zelarayán, LC (Corresponding Author), German Ctr Cardiovasc Res DZHK, Partner Site, Gottingen, Germany.
   Priesmeier, Laura; Schoger, Eric; Zelarayan, Laura Cecilia, Univ Med Ctr Goettingen UMG, Inst Pharmacol \& Toxicol, D-37075 Gottingen, Germany.
   Priesmeier, Laura; Schoger, Eric; Cyganek, Lukas; Zelarayan, Laura Cecilia, German Ctr Cardiovasc Res DZHK, Partner Site, Gottingen, Germany.
   Schoger, Eric; Cyganek, Lukas, Univ Gottingen, Cluster Excellence Multiscale Bioimaging Mol Machi, Gottingen, Germany.
   Cyganek, Lukas, Univ Med Ctr Gottingen UMG, Clin Cardiol \& Pneumol, D-37075 Gottingen, Germany.},
DOI = {10.1016/j.scr.2023.103163},
EarlyAccessDate = {JUL 2023},
Article-Number = {103163},
ISSN = {1873-5061},
EISSN = {1876-7753},
Keywords-Plus = {PLATFORM},
Research-Areas = {Cell Biology; Biotechnology \& Applied Microbiology},
Web-of-Science-Categories  = {Cell \& Tissue Engineering; Biotechnology \& Applied Microbiology; Cell
   Biology},
Affiliations = {German Centre for Cardiovascular Research; University of Gottingen},
ORCID-Numbers = {Schoger, Eric/0000-0002-5485-9828},
Funding-Acknowledgement = {NIH Common Fund Regenerative Medicine Program {[}TC1133, RUCDRi002-A];
   National Center for Advancing Translational Sciences (NCATS); National
   Institute of Neurological Disorders and Stroke (NINDS) {[}50-001-21];
   Human Cell and Data Repository (NHCDR); Open Access Publication Funds of
   the Gottingen University {[}70183, RRID:Addg-ene\_70183]; DFG {[}SFB1002
   C07, SFB1002 S01, SFB1002 INF]; DZHK (German Center for Cardiovascular
   Research); GMP working cell bank (WCB)},
Funding-Text = {Generation of the GMP line LhiPSC-GR1.1 (TC1133 or RUCDRi002-A) was
   supported by the NIH Common Fund Regenerative Medicine Program, and
   reported in Stem Cell Reports (Baghbaderani et al. 2015, doi:
   10.1016/j.stemcr.2015.08.015) . The NIH Common Fund and the National
   Center for Advancing Translational Sciences (NCATS) are joint stewards
   of the LhiPSC-GR1.1 resource. The TC1133 line (Master Cell Bank Lot\#:
   50-001-21) was acquired by Repairon GmbH from the National Institute of
   Neurological Disorders and Stroke (NINDS) Human Cell and Data Repository
   (NHCDR) and processed to a GMP working cell bank (WCB) . Post production
   cells from the WBC were kindly provided by Repairon GmbH to the UMG for
   research use. We thank Yvonne Hintz (Stem Cell Unit, UMG) , Gesa Homann
   and Petra Tucholla (Institute of Pharmacology and Toxicology, UMG) for
   superb technical support. We acknowledge support by the Open Access
   Publication Funds of the Gottingen University. FgH1tUTG was a gift from
   Marco Herold (Addg-ene plasmid \#70183 ; http://n2t.net/addgene:70183 ;
   RRID:Addg-ene\_70183) . This work was supported by the DFG grant SFB1002
   C07; SFB1002 S01 to LC; SFB1002 INF to LCZ and the DZHK (German Center
   for Cardiovascular Research) .},
Number-of-Cited-References = {5},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Stem Cell Res.},
Doc-Delivery-Number = {N9AE4},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001039846900001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000299630600035,
Author = {Jones, Philip and Binns, David and McMenamin, Conor and McAnulla, Craig
   and Hunter, Sarah},
Title = {The InterPro BioMart: federated query and web service access to the
   InterPro Resource},
Journal = {DATABASE-THE JOURNAL OF BIOLOGICAL DATABASES AND CURATION},
Year = {2011},
Abstract = {The InterPro BioMart provides users with query-optimized access to
   predictions of family classification, protein domains and functional
   sites, based on a broad spectrum of integrated computational models
   ('signatures') that are generated by the InterPro member databases:
   Gene3D, HAMAP, PANTHER, Pfam, PIRSF, PRINTS, ProDom, PROSITE, SMART,
   SUPERFAMILY and TIGRFAMs. These predictions are provided for all protein
   sequences from both the UniProt Knowledge Base and the UniParc protein
   sequence archive. The InterPro BioMart is supplementary to the primary
   InterPro web interface (http://www.ebi.ac.uk/interpro), providing a web
   service and the ability to build complex, custom queries that can
   efficiently return thousands of rows of data in a variety of formats.
   This article describes the information available from the InterPro
   BioMart and illustrates its utility with examples of how to build
   queries that return useful biological information. Database URL:
   http://www.ebi.ac.uk/interpro/biomart/martview.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Jones, P (Corresponding Author), EMBL European Bioinformat Inst, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Jones, Philip; Binns, David; McMenamin, Conor; McAnulla, Craig; Hunter, Sarah, EMBL European Bioinformat Inst, Cambridge CB10 1SD, England.},
DOI = {10.1093/database/bar033},
Article-Number = {bar033},
ISSN = {1758-0463},
Keywords-Plus = {PROTEIN FAMILIES; DATABASE; ANNOTATION; GENOMES; SYSTEM},
Research-Areas = {Mathematical \& Computational Biology},
Web-of-Science-Categories  = {Mathematical \& Computational Biology},
Author-Email = {pjones@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL)},
ORCID-Numbers = {Hunter, Sarah/0000-0003-2453-0770},
Funding-Acknowledgement = {Biotechnology and Biological Sciences Research Council {[}BB/F010508/1];
   European Union; IMproving Protein Annotation and Co-ordination using
   Technology (IMPACT) {[}213037]; BBSRC {[}BB/F010508/1] Funding Source:
   UKRI; Biotechnology and Biological Sciences Research Council
   {[}BB/F010508/1] Funding Source: researchfish},
Funding-Text = {Biotechnology and Biological Sciences Research Council's Bioinformatics
   and Biological Resources Fund (grant number BB/F010508/1); European
   Union under the program `FP7 capacities: Scientific Data Repositories';
   The working title for the project is IMproving Protein Annotation and
   Co-ordination using Technology (IMPACT) (grant number 213037). Funding
   for open access charge: European Union under the program `FP7
   capacities: Scientific Data Repositories'; The working title for the
   project is IMproving Protein Annotation and Co-ordination using
   Technology (IMPACT) (grant number 213037).},
Number-of-Cited-References = {19},
Times-Cited = {10},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {Database},
Doc-Delivery-Number = {883JQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000299630600035},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000462109900016,
Author = {Matusz, Pawel J. and Merkley, Rebecca and Faure, Michelle and Scerif,
   Gaia},
Title = {Expert attention: Attentional allocation depends on the differential
   development of multisensory number representations},
Journal = {COGNITION},
Year = {2019},
Volume = {186},
Pages = {171-177},
Month = {MAY},
Abstract = {Traditional models developed within cognitive psychology suggest that
   attention is deployed flexibly and irrespective of differences in
   expertise with to-be-attended stimuli. However, everyday environments
   are inherently multisensory and observers differ in familiarity with
   particular unisensory representations (e.g., number words, in contrast
   with digits). To test whether the predictions of the traditional models
   extend to such naturalistic settings, six-year-olds, 11-year-olds and
   young adults (N = 83) searched for predefined numerals amongst a small
   or large number of distractor digits, while distractor number words,
   digits or their combination were presented peripherally. Concurrently
   presented number words and audiovisual stimuli that were compatible with
   the target digit facilitated young children's selective attention. In
   contrast, for older children and young adults number words and
   audiovisual stimuli that were incompatible with their visual targets
   resulted in a cost on reaction time. These findings suggest that
   multisensory and familiarity-based influences interact dynamically as
   they shape selective attention. Therefore, models of selective attention
   should include multisensory and familiarity-dependent constraints: more
   or less familiar object representations across modalities will be
   attended to differently, with their effects visible as predominant
   benefits for attention at one level but costs at another.},
Publisher = {ELSEVIER SCIENCE BV},
Address = {PO BOX 211, 1000 AE AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Matusz, PJ; Scerif, G (Corresponding Author), Univ Appl Sci Western Switzerland HES SO Valais, Informat Syst Inst, Sierre, Switzerland.
   Matusz, Pawel J., Univ Appl Sci Western Switzerland HES SO Valais, Informat Syst Inst, Sierre, Switzerland.
   Matusz, Pawel J., Univ Hosp Ctr, Neuropsychol \& Neurorehabil Serv \& Radiodiagnost, LINE Lab Invest Newophysiol, Lausanne, Switzerland.
   Matusz, Pawel J., Univ Lausanne, Lausanne, Switzerland.
   Matusz, Pawel J., Vanderbilt Univ, Dept Hearing \& Speech Sci, 221 Kirkland Hall, Nashville, TN 37235 USA.
   Merkley, Rebecca, Univ Western Ontario, Numer Cognit Lab, London, ON, Canada.
   Faure, Michelle; Scerif, Gaia, Univ Oxford, Attent Brain \& Cognit Dev Grp, Oxford, England.},
DOI = {10.1016/j.cognition.2019.01.013},
ISSN = {0010-0277},
EISSN = {1873-7838},
Keywords = {Attention; Multisensory; Number words; Numerals; Children},
Keywords-Plus = {SELECTIVE ATTENTION; PERCEPTUAL LOAD; CAPTURE; MEMORY; DISTRACTION;
   ASSOCIATION; MAGNITUDE; COUNT; HEAR; CUES},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Experimental},
Author-Email = {pawel.matusz@hevs.ch
   gaia.scerif@psy.ox.ac.uk},
Affiliations = {University of Applied Sciences \& Arts Western Switzerland; University
   of Lausanne; Vanderbilt University; Western University (University of
   Western Ontario); University of Oxford},
ResearcherID-Numbers = {Matusz, Paul/AAL-7844-2020},
ORCID-Numbers = {Matusz, Paul/0000-0003-1721-4868},
Funding-Acknowledgement = {Pierre Mercier Foundation; Fondation Asile des Aveugles; Swiss National
   Science Foundation {[}PZ00P1\_174150]; James S. McDonnell Foundation;
   Swiss National Science Foundation (SNF) {[}PZ00P1\_174150] Funding
   Source: Swiss National Science Foundation (SNF)},
Funding-Text = {PJM is funded by the Pierre Mercier Foundation, Fondation Asile des
   Aveugles and the Swiss National Science Foundation (grant
   PZ00P1\_174150). G.S. was supported by a 2012 Scholar Award
   (Understanding Human Cognition) of the James S. McDonnell Foundation.
   Unfortunately, the current data set was acquired before both researchers
   and the broader public began to understand the scientific importance of
   data sharing. As we had not consented participating parents and children
   with an explicit data sharing statement, we cannot upload the current
   data set to an open data repository. Researchers interested in analysing
   the current data set are very welcome to contact the Corresponding
   Author (gaia.scerif@psy.ox.ac.uk) for data sharing.},
Number-of-Cited-References = {42},
Times-Cited = {12},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {23},
Journal-ISO = {Cognition},
Doc-Delivery-Number = {HQ0UG},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000462109900016},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000669541400016,
Author = {Cuevas-Zuviria, Bruno and Pacios, Luis F.},
Title = {Machine Learning of Analytical Electron Density in Large Molecules
   Through Message-Passing},
Journal = {JOURNAL OF CHEMICAL INFORMATION AND MODELING},
Year = {2021},
Volume = {61},
Number = {6},
Pages = {2658-2666},
Month = {JUN 28},
Abstract = {Machine learning milestones in computational chemistry are overshadowed
   by their unaccountability and the overwhelming zoo of tools for each
   specific task. A promising path to tackle these problems is using
   machine learning to reproduce physical magnitudes as a basis to derive
   many other properties. By using a model of the electron density
   consisting of an analytical expansion on a linear set of isotropic and
   anisotropic functions, we implemented in this work a message-passing
   neural network able to reproduce electron density in molecules with just
   a 2.5\% absolute error in complex cases. We also adapted our methodology
   to describe electron density in large biomolecules (proteins) and to
   obtain atomic charges, interaction energies, and DFT energies. We show
   that electron density learning is a new promising avenue with a variety
   of forthcoming applications.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Cuevas-Zuviría, B; Pacios, LF (Corresponding Author), Univ Politecn Madrid UPM, Ctr Biotecnol \& Genom Plantas CBGP, Inst Nacl Invest \& Tecnol Agr \& Alimentaria INIA, UPM INIA, Campus Montegancedo UPM, Madrid 28223, Spain.
   Pacios, LF (Corresponding Author), Univ Politecn Madrid UPM, Dept Biotecnol Biol Vegetal, Alimentaria \& Biosistemas ETSIAAB, Escuela Tecn Super Ingn Agr, Madrid 28040, Spain.
   Cuevas-Zuviria, Bruno; Pacios, Luis F., Univ Politecn Madrid UPM, Ctr Biotecnol \& Genom Plantas CBGP, Inst Nacl Invest \& Tecnol Agr \& Alimentaria INIA, UPM INIA, Campus Montegancedo UPM, Madrid 28223, Spain.
   Pacios, Luis F., Univ Politecn Madrid UPM, Dept Biotecnol Biol Vegetal, Alimentaria \& Biosistemas ETSIAAB, Escuela Tecn Super Ingn Agr, Madrid 28040, Spain.},
DOI = {10.1021/acs.jcim.1c00227},
EarlyAccessDate = {MAY 2021},
ISSN = {1549-9596},
EISSN = {1549-960X},
Keywords-Plus = {PREDICTION; BENCHMARK},
Research-Areas = {Pharmacology \& Pharmacy; Chemistry; Computer Science},
Web-of-Science-Categories  = {Chemistry, Medicinal; Chemistry, Multidisciplinary; Computer Science,
   Information Systems; Computer Science, Interdisciplinary Applications},
Author-Email = {bruno.czuviria@upm.es
   luis.fpacios@upm.es},
Affiliations = {Universidad Politecnica de Madrid; Centro de Investigacion en
   Biotecnologia Genomica de Plantas (CBGP); Instituto Nacional
   Investigacion Tecnologia Agraria Alimentaria (INIA); Universidad
   Politecnica de Madrid},
ResearcherID-Numbers = {Pacios, Luis F./I-5164-2015},
ORCID-Numbers = {Pacios, Luis F./0000-0002-0585-4289},
Funding-Acknowledgement = {Spanish Ministerio de Ciencia e Innovacion {[}BIO2017-84548R];
   predoctoral Programa Propio Grant; Universidad Politecnica de Madrid;
   Banco Santander; Agencia Estatal de Investigacion of Spain
   {[}SEV-2016-0672]},
Funding-Text = {This research was funded by the Spanish Ministerio de Ciencia e
   Innovacion, grant number BIO2017-84548R. B.C.-Z. received fund support
   from a predoctoral Programa Propio Grant, Universidad Politecnica de
   Madrid and Banco Santander. The authors acknowledge the ``Severo Ochoa
   Program for Centres of Excellence in R\&D{''} from the Agencia Estatal
   de Investigacion of Spain (grant SEV-2016-0672, 2017-2021) for
   supporting the services provided by the computation cluster of the CBGP.
   The code of our method as well as instructions to use it are available
   at GitHub. All of the data sets created to train and test our models as
   explained in the Methods, section Training and Data, are made public at
   the Zenodo open data repository maintained by CERN.},
Number-of-Cited-References = {48},
Times-Cited = {14},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {11},
Journal-ISO = {J. Chem Inf. Model.},
Doc-Delivery-Number = {TD8AA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000669541400016},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000413415700001,
Author = {Stroeve, Julienne C. and Mioduszewski, John R. and Rennermalm, Asa and
   Boisvert, Linette N. and Tedesco, Marco and Robinson, David},
Title = {Investigating the local-scale influence of sea ice on Greenland surface
   melt},
Journal = {CRYOSPHERE},
Year = {2017},
Volume = {11},
Number = {5},
Pages = {2363-2381},
Month = {OCT 23},
Abstract = {Rapid decline in Arctic sea ice cover in the 21st century may have
   wide-reaching effects on the Arctic climate system, including the
   Greenland ice sheet mass balance. Here, we investigate whether local
   changes in sea ice around the Greenland ice sheet have had an impact on
   Greenland surface melt. Specifically, we investigate the relationship
   between sea ice concentration, the timing of melt onset and open-water
   fraction surrounding Greenland with ice sheet surface melt using a
   combination of remote sensing observations, and outputs from a
   reanalysis model and a regional climate model for the period of
   1979-2015. Statistical analysis points to covariability between
   Greenland ice sheet surface melt and sea ice within Baffin Bay and Davis
   Strait. While some of this covariance can be explained by simultaneous
   influence of atmospheric circulation anomalies on both the sea ice cover
   and Greenland melt, within Baffin Bay we find a modest correlation
   between detrended melt onset over sea ice and the adjacent ice sheet
   melt onset. This correlation appears to be related to increased transfer
   of sensible and latent heat fluxes from the ocean to the atmosphere in
   early sea ice melt years, increasing temperatures and humidity over the
   ice sheet that in turn initiate ice sheet melt.},
Publisher = {COPERNICUS GESELLSCHAFT MBH},
Address = {BAHNHOFSALLEE 1E, GOTTINGEN, 37081, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Stroeve, JC (Corresponding Author), Univ Colorado, Cooperat Inst Res Environm Sci, Natl Snow \& Ice Data Ctr, 449 UCB, Boulder, CO 80309 USA.
   Stroeve, JC (Corresponding Author), UCL, Ctr Polar Observat \& Modelling, Dept Earth Sci, Gower St, London WC1E 6BT, England.
   Stroeve, Julienne C., Univ Colorado, Cooperat Inst Res Environm Sci, Natl Snow \& Ice Data Ctr, 449 UCB, Boulder, CO 80309 USA.
   Stroeve, Julienne C., UCL, Ctr Polar Observat \& Modelling, Dept Earth Sci, Gower St, London WC1E 6BT, England.
   Mioduszewski, John R., Univ Wisconsin Madison, Ctr Climat Res, 1225 W Dayton St, Madison, WI 53706 USA.
   Rennermalm, Asa; Robinson, David, Rutgers State Univ, Dept Geog, 54 Joyce Kilmer Ave, Piscataway, NJ 08854 USA.
   Boisvert, Linette N., NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA.
   Tedesco, Marco, Columbia Univ, Lamont Doherty Earth Observ, Palisades, NY 10964 USA.},
DOI = {10.5194/tc-11-2363-2017},
ISSN = {1994-0416},
EISSN = {1994-0424},
Keywords-Plus = {REGIONAL CLIMATE MODEL; MASS-BALANCE; SHEET; VARIABILITY; SIMULATION;
   ATMOSPHERE; ENERGY; COVER; SNOW; TEMPERATURE},
Research-Areas = {Physical Geography; Geology},
Web-of-Science-Categories  = {Geography, Physical; Geosciences, Multidisciplinary},
Author-Email = {stroeve@nsidc.org},
Affiliations = {University of Colorado System; University of Colorado Boulder;
   University of London; University College London; University of Wisconsin
   System; University of Wisconsin Madison; Rutgers System; Rutgers New
   Brunswick; National Aeronautics \& Space Administration (NASA); NASA
   Goddard Space Flight Center; Columbia University},
ResearcherID-Numbers = {Stroeve, Julienne/ABE-7227-2020
   Rennermalm, Asa K/I-3270-2012},
ORCID-Numbers = {Rennermalm, Asa K/0000-0002-2470-7444},
Funding-Acknowledgement = {National Science Foundation {[}PLR 1304807]; NASA ROSES IDS
   {[}12-IDS12-0120]; NERC {[}cpom30001] Funding Source: UKRI; Natural
   Environment Research Council {[}cpom30001] Funding Source: researchfish},
Funding-Text = {This work was funded by the National Science Foundation PLR 1304807. All
   data used in this study were obtained from free and open data
   repositories. Detailed information is provided in the methods section.
   The work of Linette Boisvert was funded by NASA ROSES 2012 IDS proposal
   no. 12-IDS12-0120.},
Number-of-Cited-References = {81},
Times-Cited = {26},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {26},
Journal-ISO = {Cryosphere},
Doc-Delivery-Number = {FK3WB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000413415700001},
OA = {Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000411196000020,
Author = {Mallard, C. and Jacquet, B. and Coltice, N.},
Title = {ADOPT: A tool for automatic detection of tectonic plates at the surface
   of convection models},
Journal = {GEOCHEMISTRY GEOPHYSICS GEOSYSTEMS},
Year = {2017},
Volume = {18},
Number = {8},
Pages = {3197-3208},
Month = {AUG},
Abstract = {Mantle convection models with plate-like behavior produce surface
   structures comparable to Earth's plate boundaries. However, analyzing
   those structures is a difficult task, since convection models produce,
   as on Earth, diffuse deformation and elusive plate boundaries. Therefore
   we present here and share a quantitative tool to identify plate
   boundaries and produce plate polygon layouts from results of numerical
   models of convection: Automatic Detection Of Plate Tectonics (ADOPT).
   This digital tool operates within the free open-source visualization
   software Paraview. It is based on image segmentation techniques to
   detect objects. The fundamental algorithm used in ADOPT is the watershed
   transform. We transform the output of convection models into a
   topographic map, the crest lines being the regions of deformation (plate
   boundaries) and the catchment basins being the plate interiors. We
   propose two generic protocols (the field and the distance methods) that
   we test against an independent visual detection of plate polygons. We
   show that ADOPT is effective to identify the smaller plates and to close
   plate polygons in areas where boundaries are diffuse or elusive. ADOPT
   allows the export of plate polygons in the standard OGR-GMT format for
   visualization, modification, and analysis under generic softwares like
   GMT or GPlates.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Mallard, C (Corresponding Author), Univ Lyon 1, CNRS, Ecole Normale Super Lyon, Lab Geol Lyon, Villeurbanne, France.
   Mallard, C.; Coltice, N., Univ Lyon 1, CNRS, Ecole Normale Super Lyon, Lab Geol Lyon, Villeurbanne, France.
   Jacquet, B., Kitware, Villeurbanne, France.},
DOI = {10.1002/2017GC007030},
ISSN = {1525-2027},
Keywords = {image segmentation; plate tectonics; convection models; plates layout},
Keywords-Plus = {SINGLE-SIDED SUBDUCTION; MANTLE CONVECTION; PARAMETERS; BOUNDARIES;
   BEHAVIOR; FAULTS; FLOW},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {claire.mallard@univ-lyon1.fr},
Affiliations = {Centre National de la Recherche Scientifique (CNRS); Universite Claude
   Bernard Lyon 1; Ecole Normale Superieure de Lyon (ENS de LYON); Kitware,
   Inc.},
ORCID-Numbers = {Mallard, Claire A./0000-0003-2595-2414
   Jacquet, Bastien/0000-0003-2860-3850
   Coltice, Nicolas/0000-0001-5444-414X},
Funding-Acknowledgement = {European Research Council within the framework of the SP2-Ideas
   Programme ERC-CoG under ERC {[}617588]},
Funding-Text = {We thank Thorsten Becker, Fabio Crameri, Giampiero Iaffaldano, and an
   anonymous reviewer for constructive comments that helped improve the
   manuscript. We could not test ADOPT on other codes without the help of
   Georg Stadler, Siqi Zhang, and Craig O'Neill, Fabio Crameri, Brad Foley,
   and Thorsten Becker. They kindly shared their data in the needed format.
   Finding some from almost 10 years ago is a challenge. We appreciate a
   lot and thank them very much. The research leading to these results was
   funded by the European Research Council within the framework of the
   SP2-Ideas Programme ERC-2013-CoG under ERC grant agreement 617588. The
   Virtual Box file and the Docker files can be found along with the data
   used here on the open data repository https://osf.io/dfzwn.},
Number-of-Cited-References = {30},
Times-Cited = {1},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Geochem. Geophys. Geosyst.},
Doc-Delivery-Number = {FH5HK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000411196000020},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000703845200010,
Author = {Mattoni, Matthew and Wilson, Sylia and Olino, Thomas M.},
Title = {Identifying profiles of brain structure and associations with current
   and future psychopathology in youth},
Journal = {DEVELOPMENTAL COGNITIVE NEUROSCIENCE},
Year = {2021},
Volume = {51},
Month = {OCT},
Abstract = {Brain structure is often studied as a marker of youth psychopathology by
   examining associations between volume or thickness of individual regions
   and specific diagnoses. However, these univariate approaches do not
   address whether the effect of a particular region may depend on the
   structure of other regions. Here, we identified subgroups of individuals
   with distinct profiles of brain structure and examined how these
   profiles were associated with concurrent and future youth
   psychopathology. We used latent profile analysis to identify distinct
   neuroanatomical profiles of subcortical region volume and orbitofrontal
   cortical thickness in the ABCD study (N = 9376, mean age = 9.91, SD =
   0.62). We identified a five-profile solution consisting of a reduced
   subcortical volume profile, a reduced orbitofrontal thickness profile, a
   reduced limbic and elevated striatal volume profile, an elevated
   orbitofrontal thickness and reduced striatal volume profile, and an
   elevated orbitofrontal thickness and subcortical volume profile. While
   controlling for age, sex, and intracranial volume, profiles exhibited
   differences in concurrent psychopathology measured dimensionally and
   categorically and in psychopathology at 1 year follow-up measured
   dimensionally. Results show that profiles of brain structure have
   incremental validity for associations with youth psychopathology beyond
   intracranial volume.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Mattoni, M (Corresponding Author), Temple Univ, Dept Psychol, 1701 N 13th St, Philadelphia, PA 19122 USA.
   Mattoni, Matthew; Olino, Thomas M., Temple Univ, Dept Psychol, 1701 N 13th St, Philadelphia, PA 19122 USA.
   Wilson, Sylia, Univ Minnesota, Inst Child Dev, 1 E River Rd, Minneapolis, MN 55455 USA.},
DOI = {10.1016/j.dcn.2021.101013},
EarlyAccessDate = {SEP 2021},
Article-Number = {101013},
ISSN = {1878-9293},
EISSN = {1878-9307},
Keywords = {Brain profile; Brain structure; Latent profile analysis; Youth
   psychopathology; ABCD study},
Keywords-Plus = {GRAY-MATTER VOLUME; GENERALIZED ANXIETY DISORDER; MAJOR DEPRESSIVE
   DISORDER; CORTICAL THICKNESS; EARLY-ONSET; ABNORMALITIES; METAANALYSIS;
   SCHIZOPHRENIA; MORPHOMETRY; SYMPTOMS},
Research-Areas = {Psychology; Neurosciences \& Neurology},
Web-of-Science-Categories  = {Psychology, Developmental; Neurosciences},
Author-Email = {matt.mattoni@temple.edu},
Affiliations = {Pennsylvania Commonwealth System of Higher Education (PCSHE); Temple
   University; University of Minnesota System; University of Minnesota Twin
   Cities},
ORCID-Numbers = {Mattoni, Matthew/0000-0001-8931-0707},
Funding-Acknowledgement = {National Institutes of Health; Temple University Libraries Open Access
   Publishing Fund; NIH {[}R21 AA026632, R01 MH107495];  {[}U01DA041048]; 
   {[}U01DA050989];  {[}U01DA051016];  {[}U01DA041022];  {[}U01DA051018]; 
   {[}U01DA051037];  {[}U01DA050987];  {[}U01DA041174];  {[}U01DA041106]; 
   {[}U01DA041117];  {[}U01DA041028];  {[}U01DA041134];  {[}U01DA050988]; 
   {[}U01DA051039];  {[}U01DA041156];  {[}U01DA041025];  {[}U01DA041120]; 
   {[}U01DA051038];  {[}U01DA041148];  {[}U01DA041093];  {[}U01DA041089]; 
   {[}U24DA041123];  {[}U24DA041147]},
Funding-Text = {Data used in the preparation of this article were obtained from the
   Adolescent Brain Cognitive DevelopmentSM (ABCD) Study (https://abcd
   study.org), held in the NIMH Data Archive (NDA). This is a multisite,
   longitudinal study designed to recruit more than 10,000 children age
   9-10 and follow them over 10 years into early adulthood. The ABCD Study
   (R) is supported by the National Institutes of Health and additional
   federal partners under award numbers U01DA041048, U01DA050989,
   U01DA051016, U01DA041022, U01DA051018, U01DA051037, U01DA050987,
   U01DA041174, U01DA041106, U01DA041117, U01DA041028, U01DA041134,
   U01DA050988, U01DA051039, U01DA041156, U01DA041025, U01DA041120,
   U01DA051038, U01DA041148, U01DA041093, U01DA041089, U24DA041123,
   U24DA041147. A full list of supporters is available at
   https://abcdstudy.org/federal-partners.html.A listing of participating
   sites and a complete listing of the study investigators can be found at
   https://abcdstudy.org/consortium\_members/.ABCD consortium investigators
   designed and implemented the study and/or provided data but did not
   necessarily participate in analysis or writing of this report. This
   manuscript reflects the views of the authors and may not reflect the
   opinions or views of the NIH or ABCD consortium investigators. The ABCD
   data repository grows and changes over time. The ABCD data used in this
   report came from NIMH Data Archive Digital Object Identifier DOI
   10.15154/1519007. Investigator support came from NIH grants R21 AA026632
   (Wilson) and R01 MH107495 (Olino). Publication of this article was
   funded in part by the Temple University Libraries Open Access Publishing
   Fund.},
Number-of-Cited-References = {66},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Dev. Cogn. Neurosci.},
Doc-Delivery-Number = {WB8VO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000703845200010},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000298601300045,
Author = {Hunter, Sarah and Jones, Philip and Mitchell, Alex and Apweiler, Rolf
   and Attwood, Teresa K. and Bateman, Alex and Bernard, Thomas and Binns,
   David and Bork, Peer and Burge, Sarah and de Castro, Edouard and
   Coggill, Penny and Corbett, Matthew and Das, Ujjwal and Daugherty,
   Louise and Duquenne, Lauranne and Finn, Robert D. and Fraser, Matthew
   and Gough, Julian and Haft, Daniel and Hulo, Nicolas and Kahn, Daniel
   and Kelly, Elizabeth and Letunic, Ivica and Lonsdale, David and Lopez,
   Rodrigo and Madera, Martin and Maslen, John and McAnulla, Craig and
   McDowall, Jennifer and McMenamin, Conor and Mi, Huaiyu and
   Mutowo-Muellenet, Prudence and Mulder, Nicola and Natale, Darren and
   Orengo, Christine and Pesseat, Sebastien and Punta, Marco and Quinn,
   Antony F. and Rivoire, Catherine and Sangrador-Vegas, Amaia and
   Selengut, Jeremy D. and Sigrist, Christian J. A. and Scheremetjew, Maxim
   and Tate, John and Thimmajanarthanan, Manjulapramila and Thomas, Paul D.
   and Wu, Cathy H. and Yeats, Corin and Yong, Siew-Yit},
Title = {InterPro in 2011: new developments in the family and domain prediction
   database},
Journal = {NUCLEIC ACIDS RESEARCH},
Year = {2012},
Volume = {40},
Number = {D1},
Pages = {D306-D312},
Month = {JAN},
Abstract = {InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates
   diverse information about protein families, domains and functional
   sites, and makes it freely available to the public via Web-based
   interfaces and services. Central to the database are diagnostic models,
   known as signatures, against which protein sequences can be searched to
   determine their potential function. InterPro has utility in the
   large-scale analysis of whole genomes and meta-genomes, as well as in
   characterizing individual protein sequences. Herein we give an overview
   of new developments in the database and its associated software since
   2009, including updates to database content, curation processes and Web
   and programmatic interfaces.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Hunter, S (Corresponding Author), EMBL, Outstat European Bioinformat Inst EBI, Wellcome Trust Genome Campus, Cambridge CB10 1SD, England.
   Hunter, Sarah; Jones, Philip; Mitchell, Alex; Apweiler, Rolf; Binns, David; Burge, Sarah; Corbett, Matthew; Das, Ujjwal; Daugherty, Louise; Fraser, Matthew; Lonsdale, David; Lopez, Rodrigo; Maslen, John; McAnulla, Craig; McDowall, Jennifer; McMenamin, Conor; Mutowo-Muellenet, Prudence; Pesseat, Sebastien; Quinn, Antony F.; Sangrador-Vegas, Amaia; Scheremetjew, Maxim; Thimmajanarthanan, Manjulapramila; Yong, Siew-Yit, EMBL, Outstat European Bioinformat Inst EBI, Cambridge CB10 1SD, England.
   Attwood, Teresa K., Univ Manchester, Fac Life Sci, Manchester M13 9PL, Lancs, England.
   Attwood, Teresa K., Univ Manchester, Sch Comp Sci, Manchester M13 9PL, Lancs, England.
   Bateman, Alex; Coggill, Penny; Finn, Robert D.; Punta, Marco; Tate, John, Wellcome Trust Sanger Inst, Cambridge CB10 1SA, England.
   Bernard, Thomas; Duquenne, Lauranne; Kahn, Daniel, Univ Lyon 1, CNRS, INRA, PRABI, F-69622 Villeurbanne, France.
   Bernard, Thomas; Duquenne, Lauranne; Kahn, Daniel, Univ Lyon 1, CNRS, INRA, Lab Biometrie \& Biol Evolut, F-69622 Villeurbanne, France.
   Bork, Peer; Letunic, Ivica, European Mol Lab EMBL, D-69117 Heidelberg, Germany.
   de Castro, Edouard; Hulo, Nicolas; Rivoire, Catherine; Sigrist, Christian J. A., CMU, SIB, Geneva 4, Switzerland.
   Gough, Julian; Madera, Martin, Univ Bristol, Dept Comp Sci, Bristol BS8 1UB, Avon, England.
   Haft, Daniel; Selengut, Jeremy D., JCVI, Rockville, MD 20850 USA.
   Kelly, Elizabeth; Mulder, Nicola, Univ Cape Town, Inst Infect Dis \& Mol Med, Computat Biol Unit, ZA-7925 Observatory, South Africa.
   Mi, Huaiyu; Thomas, Paul D., Univ So Calif, Los Angeles, CA 90089 USA.
   Natale, Darren, Georgetown Univ, Med Ctr, PIR, Washington, DC 20007 USA.
   Orengo, Christine; Wu, Cathy H.; Yeats, Corin, Univ London, Univ Coll London, Struct \& Mol Biol Dept, London WC1E 6BT, England.},
DOI = {10.1093/nar/gkr948},
ISSN = {0305-1048},
EISSN = {1362-4962},
Keywords-Plus = {GENE ONTOLOGY; PROTEIN FAMILIES; ANNOTATION; FRAMEWORK; PATHWAYS},
Research-Areas = {Biochemistry \& Molecular Biology},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology},
Author-Email = {hunter@ebi.ac.uk
   pjones@ebi.ac.uk
   mitchell@ebi.ac.uk},
Affiliations = {European Molecular Biology Laboratory (EMBL); University of Manchester;
   University of Manchester; Wellcome Trust Sanger Institute; Centre
   National de la Recherche Scientifique (CNRS); Universite Claude Bernard
   Lyon 1; INRAE; INRAE; VetAgro Sup; Centre National de la Recherche
   Scientifique (CNRS); Universite Claude Bernard Lyon 1; European
   Molecular Biology Laboratory (EMBL); Swiss Institute of Bioinformatics;
   University of Bristol; J. Craig Venter Institute; University of Cape
   Town; University of Southern California; Georgetown University;
   University of London; University College London},
ResearcherID-Numbers = {Natale, Darren A/AAE-9303-2019
   Kahn, Daniel/B-9393-2013
   Punta, Marco/ABH-4698-2020
   Letunic, Ivica/K-1102-2019
   Bateman, Alex/H-2861-2019
   Letunic, Ivica/A-6032-2009
   Mulder, Nicola J/JFS-0309-2023
   Bork, Peer/F-1813-2013
   Crozier, Laura B./A-4821-2010
   Wu, Chih-Hang John/C-2518-2015
   Lopez, Rodrigo/AAC-6111-2019
   Tate, John/ABE-5666-2021
   },
ORCID-Numbers = {Natale, Darren A/0000-0001-5809-9523
   Kahn, Daniel/0000-0001-8093-0854
   Punta, Marco/0000-0002-0050-0676
   Letunic, Ivica/0000-0003-3560-4288
   Bateman, Alex/0000-0002-6982-4660
   Mulder, Nicola J/0000-0003-4905-0941
   Bork, Peer/0000-0002-2627-833X
   Wu, Chih-Hang John/0000-0001-9929-4421
   Lopez, Rodrigo/0000-0003-1256-7306
   Tate, John/0000-0002-8315-6574
   Mutowo, Prudence/0000-0002-4646-4172
   Finn, Robert D./0000-0001-8626-2148
   Yong, Siew Yit/0000-0002-1952-3528
   Fraser, Matthew/0000-0003-2318-9080
   Bernard, Thomas/0000-0003-3736-1507
   SIGRIST, Christian J. A./0000-0002-4348-0070
   Rivoire, Catherine/0000-0002-5979-8382
   Daugherty, Louise/0000-0003-4546-6667
   Scheremetjew, Maxim/0000-0002-7458-3072
   de Castro, Edouard/0000-0001-5436-7383
   Sangrador, Amaia/0000-0001-6688-429X
   Burge, Sarah/0000-0002-2506-927X
   Wu, Cathy/0000-0001-6379-8601
   Thomas, Paul/0000-0002-9074-3507
   Apweiler, Rolf/0000-0001-7078-200X
   Mitchell, Alex/0000-0001-8655-7966
   Attwood, Teresa/0000-0003-2409-4235
   Quinn, Antony/0000-0002-0596-7638
   Hunter, Sarah/0000-0003-2453-0770},
Funding-Acknowledgement = {European Union {[}213037]; BBSRC {[}BB/F010508/1]; United States
   National Institutes of Health {[}GM081084]; EMBL-EBI; Biotechnology and
   Biological Sciences Research Council {[}BB/F010508/1, BB/G022771/1,
   BB/F010435/1] Funding Source: researchfish; BBSRC {[}BB/F010435/1,
   BB/F010508/1, BB/G022771/1] Funding Source: UKRI},
Funding-Text = {European Union under the program `FP7 capacities: Scientific Data
   Repositories' (grant number 213037). The title for the project is
   IMproving Protein Annotation and Co-ordination using Technology
   (IMPACT); BBSRC Bioinformatics and Biological Resources Fund (grant
   BB/F010508/1); and improvements to InterProScan have been supported in
   part by a grant from the United States National Institutes of Health
   (grant GM081084). Funding for open access charge: EMBL-EBI.},
Number-of-Cited-References = {28},
Times-Cited = {823},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {110},
Journal-ISO = {Nucleic Acids Res.},
Doc-Delivery-Number = {869MD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000298601300045},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000362125300043,
Author = {Gershman, Daniel J. and Dorelli, John C. and F-Vinas, Adolfo and
   Pollock, Craig J.},
Title = {The calculation of moment uncertainties from velocity distribution
   functions with random errors},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2015},
Volume = {120},
Number = {8},
Pages = {6633-6645},
Month = {AUG},
Abstract = {Instrumentation that detects individual plasma particles is susceptible
   to random counting errors. These errors propagate into the calculations
   of moments of measured particle velocity distribution functions.
   Although rules of thumb exist for the effects of random errors on the
   calculation of lower order moments (e.g., density, velocity, and
   temperature) of Maxwell-Boltzmann distributions, they do not generally
   apply to nonthermal distributions or to higher-order moments. To date,
   such errors have only been estimated using brute force Monte Carlo
   techniques, i.e., repeated (similar to 50) samplings of distribution
   functions. Here we present a mathematical formalism for analytically
   obtaining uncertainty estimates of plasma moments due to random errors
   either measured in situ by instruments or synthesized by particle
   simulations. Our uncertainty estimates precisely match the statistical
   variation of simulated plasma moments and carry the computational cost
   equivalent of only similar to 15 Monte Carlo samplings. In addition, we
   provide the means to calculate a covariance matrix that can be reported
   along with typical plasma moments. This matrix enables the propagation
   of statistical errors into arbitrary coordinate systems or functions of
   plasma moments without the need to reanalyze full distribution
   functions. Our methodology, which is applied to electron data from
   Plasma Electron and Current Experiment on the Cluster spacecraft as an
   example, is relevant to both existing and future data sets and requires
   only instrument-measured counts and phase space densities reported for a
   set of calibrated energy-angle targets.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Gershman, DJ (Corresponding Author), NASA, Goddard Space Flight Ctr, Geospace Phys Lab, Greenbelt, MD 20771 USA.
   Gershman, Daniel J.; Dorelli, John C.; F-Vinas, Adolfo; Pollock, Craig J., NASA, Goddard Space Flight Ctr, Geospace Phys Lab, Greenbelt, MD 20771 USA.},
DOI = {10.1002/2014JA020775},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords = {particle instrumentation; plasma moments; velocity distribution
   function; random errors},
Keywords-Plus = {IN-FLIGHT CALIBRATION; CLUSTER; MAGNETOSHEATH; SPECTROMETER; INSTRUMENT;
   SATELLITE; ELECTRONS; PLASMAS; PEACE},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {daniel.j.gershman@nasa.gov},
Affiliations = {National Aeronautics \& Space Administration (NASA); NASA Goddard Space
   Flight Center},
ResearcherID-Numbers = {Dorelli, John C./C-9488-2012
   },
ORCID-Numbers = {Dorelli, John/0000-0003-0475-6545},
Funding-Acknowledgement = {Magnetospheric Multiscale Mission {[}WBS 943396.05.03.02.10.01]; Science
   and Technology Facilities Council {[}ST/G008493/1, ST/H004130/1] Funding
   Source: researchfish; UK Space Agency {[}ST/N003586/1, ST/J004758/1]
   Funding Source: researchfish; STFC {[}ST/G008493/1, ST/H004130/1]
   Funding Source: UKRI},
Funding-Text = {The high-resolution electron data used in this work were obtained from
   Mullard Space Science Laboratory. Cluster/PEACE data were obtained from
   the open data repository via the UDF software data analysis package, and
   the magnetic field data were obtained from the Cluster/FGM prime
   parameters. The IDL software used to generate uncertainty estimates for
   velocity moments is included online as supporting information. The
   numerical data generated for this paper will be made available upon
   request. The authors wish to thank the members of the FPI ground
   operations and science team for their feedback and support. This work
   was supported by the Magnetospheric Multiscale Mission under WBS
   943396.05.03.02.10.01 for the Fast Plasma Instrument. D.J.G. is
   supported by an appointment to the NASA Postdoctoral Program at Goddard
   Space Flight Center, administered by Oak Ridge Associated Universities.},
Number-of-Cited-References = {33},
Times-Cited = {33},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {CS5NP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000362125300043},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000407790400001,
Author = {Sato, Natsuo and Yukimatu, Akira Sessai and Tanaka, Yoshimasa and Hori,
   Tomoaki},
Title = {Morphologies of omega band auroras},
Journal = {EARTH PLANETS AND SPACE},
Year = {2017},
Volume = {69},
Month = {AUG 3},
Abstract = {We examined the morphological signatures of 315 omega band aurora events
   observed using the Time History of Events and Macroscale Interactions
   during Substorm ground-based all-sky imager network over a period of 8
   years. We find that omega bands can be classified into the following
   three subtypes: (1) classical (O-type) omega bands, (2) torch or tongue
   (T-type) omega bands, and (3) combinations of classical and torch or
   tongue (O/T-type) omega bands. The statistical results show that T-type
   bands occur the most frequently (45\%), followed by O/T-type bands
   (35\%) and O-type bands (18\%). We also examined the morphologies of the
   omega bands during their formation, from the growth period to the
   declining period through the maximum period. Interestingly, the omega
   bands are not stable, but rather exhibit dynamic changes in shape,
   intensity, and motion. They grow from small-scale bumps (seeds) at the
   poleward boundary of preexisting east-west-aligned auroras, rather than
   via the rotation or shear motion of preexisting east-west-aligned
   auroras, and do not exhibit any shear motion during the periods of
   auroral activity growth. Furthermore, the auroral luminosity is observed
   to increase during the declining period, and the total time from the
   start of the growth period to the end of the declining period is found
   to be about 20 min. Such dynamical signatures may be important in
   determining the mechanism responsible for omega band formation.},
Publisher = {SPRINGEROPEN},
Address = {CAMPUS, 4 CRINAN ST, LONDON, N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Sato, N (Corresponding Author), Natl Inst Polar Res, Tokyo, Japan.
   Sato, Natsuo; Yukimatu, Akira Sessai; Tanaka, Yoshimasa, Natl Inst Polar Res, Tokyo, Japan.
   Sato, Natsuo; Yukimatu, Akira Sessai; Tanaka, Yoshimasa, SOKENDAI Grad Univ Adv Studies, Hayama, Kanagawa, Japan.
   Hori, Tomoaki, Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan.
   Hori, Tomoaki, Univ Tokyo, Grad Sch Sci, Dept Earth \& Planetary Sci, Tokyo, Japan.},
DOI = {10.1186/s40623-017-0688-1},
Article-Number = {103},
ISSN = {1880-5981},
Keywords = {Omega band aurora; Torch aurora; Tongue aurora; Pulsating aurora;
   All-sky imager; THEMIS; Ionosphere; Magnetosphere; Field-aligned current},
Keywords-Plus = {ELECTRODYNAMICS},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {nsato@nipr.ac.jp},
Affiliations = {Research Organization of Information \& Systems (ROIS); National
   Institute of Polar Research (NIPR) - Japan; Graduate University for
   Advanced Studies - Japan; Nagoya University; University of Tokyo},
ORCID-Numbers = {Hori, Tomoaki/0000-0001-8451-6941},
Funding-Acknowledgement = {Inter-university Upper atmosphere Global Observation NETwork (IUGONET) -
   Ministry of Education, Culture, Sports, Science and Technology of Japan;
   CSA {[}9F007-046101]; NASA {[}NAS5-02099];  {[}15K05305];  {[}25287129];
   Grants-in-Aid for Scientific Research {[}17K05672, 15H02628, 25287129]
   Funding Source: KAKEN},
Funding-Text = {This work was partially supported by a Grant-in-Aid for Scientific
   Research C (15K05305), B (25287129) and the Inter-university Upper
   atmosphere Global Observation NETwork (IUGONET) project funded by the
   Ministry of Education, Culture, Sports, Science and Technology of Japan.
   We would like to thank A. Kadokura for useful comments. Part of the work
   of TH has been conducted at ERG-Science Center (ERG-SC) operated by
   ISAS/JAXA and ISEE/Nagoya University. The authors acknowledge NASA
   contract NAS5-02099 for the use of data from the THEMIS Mission.
   Specifically, we thank S. Mende and E. Donovan for use of the ASI data.
   Deployment and data retrieval of the THEMIS ASIs were partly supported
   by CSA contract 9F007-046101. THEMIS all-sky image data are available
   through the open data repository at UC Berkeley at
   http://themis.ssl.berkeley.edu/index.shtml.},
Number-of-Cited-References = {21},
Times-Cited = {6},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Earth Planets Space},
Doc-Delivery-Number = {FD8QY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000407790400001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000381629900001,
Author = {Mioduszewski, J. R. and Rennermalm, A. K. and Hammann, A. and Tedesco,
   M. and Noble, E. U. and Stroeve, J. C. and Mote, T. L.},
Title = {Atmospheric drivers of Greenland surface melt revealed by
   self-organizing maps},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES},
Year = {2016},
Volume = {121},
Number = {10},
Pages = {5095-5114},
Month = {MAY 27},
Abstract = {Recent acceleration in surface melt on the Greenland ice sheet (GrIS)
   has occurred concurrently with a rapidly warming Arctic and has been
   connected to persistent, anomalous atmospheric circulation patterns over
   Greenland. To identify synoptic setups favoring enhanced GrIS surface
   melt and their decadal changes, we develop a summer Arctic synoptic
   climatology by employing self-organizing maps. These are applied to
   daily 500 hPa geopotential height fields obtained from the Modern Era
   Retrospective Analysis for Research and Applications reanalysis,
   1979-2014. Particular circulation regimes are related to meteorological
   conditions and GrIS surface melt estimated with outputs from the Modele
   Atmospherique Regional. Our results demonstrate that the largest
   positive melt anomalies occur in concert with positive height anomalies
   near Greenland associated with wind, temperature, and humidity patterns
   indicative of strong meridional transport of heat and moisture. We find
   an increased frequency in a 500 hPa ridge over Greenland coinciding with
   a 63\% increase in GrIS melt between the 1979-1988 and 2005-2014
   periods, with 75.0\% of surface melt changes attributed to
   thermodynamics, 17\% to dynamics, and 8.0\% to a combination. We also
   confirm that the 2007-2012 time period has the largest dynamic forcing
   relative of any period but also demonstrate that increased surface
   energy fluxes, temperature, and moisture separate from dynamic changes
   contributed more to melt even during this period. This implies that GrIS
   surface melt is likely to continue to increase in response to an ever
   warmer future Arctic, regardless of future atmospheric circulation
   patterns.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Mioduszewski, JR (Corresponding Author), Univ Wisconsin, Ctr Climat Res, Madison, WI 53706 USA.
   Mioduszewski, JR (Corresponding Author), Rutgers State Univ, Dept Geog, New Brunswick, NJ 08901 USA.
   Mioduszewski, J. R., Univ Wisconsin, Ctr Climat Res, Madison, WI 53706 USA.
   Mioduszewski, J. R.; Rennermalm, A. K.; Hammann, A., Rutgers State Univ, Dept Geog, New Brunswick, NJ 08901 USA.
   Tedesco, M.; Noble, E. U., NASA, Goddard Inst Space Studies, New York, NY 10025 USA.
   Tedesco, M., Columbia Univ, Lamont Doherty Earth Observ, Palisades, NY USA.
   Stroeve, J. C., Natl Snow \& Ice Data Ctr, Boulder, CO USA.
   Stroeve, J. C., UCL, Ctr Polar Observat \& Modelling Pearson Bldg, London, England.
   Mote, T. L., Univ Georgia, Dept Geog, Athens, GA 30602 USA.},
DOI = {10.1002/2015JD024550},
ISSN = {2169-897X},
EISSN = {2169-8996},
Keywords-Plus = {REGIONAL CLIMATE MODEL; ICE-SHEET; MASS-BALANCE; MIDTROPOSPHERIC
   CIRCULATION; WEST GREENLAND; SIMULATION; TRENDS; ENERGY; VARIABILITY;
   PATTERNS},
Research-Areas = {Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Meteorology \& Atmospheric Sciences},
Author-Email = {jmioduszewsk@wisc.edu},
Affiliations = {University of Wisconsin System; University of Wisconsin Madison; Rutgers
   System; Rutgers New Brunswick; National Aeronautics \& Space
   Administration (NASA); NASA Goddard Space Flight Center; Goddard
   Institute for Space Studies; Columbia University; University of London;
   University College London; University System of Georgia; University of
   Georgia},
ResearcherID-Numbers = {Stroeve, Julienne/ABE-7227-2020
   Rennermalm, Asa K/I-3270-2012
   Mote, Thomas/U-6681-2017},
ORCID-Numbers = {Rennermalm, Asa K/0000-0002-2470-7444
   Mote, Thomas/0000-0002-0021-0134},
Funding-Acknowledgement = {NSF {[}PLR-1304805, PLR-1304807]; NASA {[}NNX14AD98G]; Natural
   Environment Research Council {[}cpom30001] Funding Source: researchfish;
   Office of Polar Programs (OPP); Directorate For Geosciences {[}1304807]
   Funding Source: National Science Foundation; NASA {[}685444, NNX14AD98G]
   Funding Source: Federal RePORTER; NERC {[}cpom30001] Funding Source:
   UKRI},
Funding-Text = {J.R. Mioduszewski and A.K. Rennermalm were funded by NSF PLR-1304805. M.
   Tedesco and E.U. Noble were funded by NSF PLR-1304807 and NASA
   NNX14AD98G. We thank three anonymous reviewers for their constructive
   comments and insights to strengthen this paper. All data used in this
   study were obtained from free and open data repositories. Detailed
   information is provided in the methods section.},
Number-of-Cited-References = {73},
Times-Cited = {33},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {24},
Journal-ISO = {J. Geophys. Res.-Atmos.},
Doc-Delivery-Number = {DT6YB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000381629900001},
OA = {Green Published, Green Submitted, Bronze},
DA = {2024-01-15},
}

@article{ WOS:000657550400009,
Author = {Christophe, Virginie and Hansenne, Michel},
Title = {Negative Valence Effect in Affective Forecasting: The Unique Impact of
   the Valence Among Dispositional and Contextual Factors for Certain Life
   Events},
Journal = {EUROPES JOURNAL OF PSYCHOLOGY},
Year = {2021},
Volume = {17},
Number = {2},
Pages = {117-130},
Month = {MAY},
Abstract = {Decades of research on affective forecasting have shown a persistent
   intensity bias-a strong tendency by which people overestimate their
   future hedonic response for positive events and underestimate it for
   negatives one. While previous research has provided answers on the
   isolated impact of various individual or contextual factors, this study
   is original in that it brings them together to determine which ones most
   influence the inaccuracy of affective forecasting. Participants were
   asked to predict their emotional satisfaction for a personal life event,
   the course (positive or negative) and date of which were already known.
   First, the results support previous research by showing that affective
   predictions are highly associated with people's affective experience.
   Moreover, multiple regression showed that among the individual and
   contextual factors previously reported to be in relation with affective
   forecasting inaccuracy, only the valence of the event could explain
   inaccuracy of forecasting. According to a growing body of literature,
   these findings point out a tendency to underestimate the intensity of
   the affect predicted both for negative and positive, with a stronger
   underestimation for negative events: the negative valence effect.},
Publisher = {PSYCHOPEN},
Address = {UNIVERSITAETSRING 15, TRIER, 54296, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Christophe, V (Corresponding Author), Univ Liege, Pl 20 Aout 7 Bat A1, B-4000 Liege, Belgium.
   Christophe, Virginie; Hansenne, Michel, Univ Liege, PsyNCog Res Unit, Liege, Belgium.},
DOI = {10.5964/ejop.1945},
ISSN = {1841-0413},
Keywords = {affective forecasting; intensity bias; negative valence effect},
Keywords-Plus = {EMOTIONAL INTELLIGENCE; DURABILITY BIAS; INTENSITY BIAS; ACCURACY; TIME;
   RELIABILITY; VALIDATION; HAPPINESS; OPTIMISM; NEGLECT},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Multidisciplinary},
Author-Email = {v.christophe@uliege.be},
Affiliations = {University of Liege},
ResearcherID-Numbers = {Hansenne, Michel/D-2138-2015},
ORCID-Numbers = {Hansenne, Michel/0000-0002-3478-4953},
Funding-Acknowledgement = {University of Liege {[}NFB-14/19]},
Funding-Text = {This research was funded by the University of Liege under Grant Number
   NFB-14/19, and meets its expectations in regards to research data, which
   are available in the Open Science Framework (OSF) public data
   repository.},
Number-of-Cited-References = {55},
Times-Cited = {2},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Eur. J. Psychol.},
Doc-Delivery-Number = {SM4AM},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:000657550400009},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000436077500006,
Author = {Canales-Garcia, I and Urrutia-Fucugauchi, J. and Aguayo-Camargo, E.},
Title = {Seismic imaging and attribute analysis of Chicxulub Crater central
   sector, Yucatan Platform, Gulf of Mexico},
Journal = {GEOLOGICA ACTA},
Year = {2018},
Volume = {16},
Number = {2},
Pages = {215-235},
Month = {JUN},
Abstract = {Chicxulub Crater, formed similar to 66Ma ago by an asteroid impact on
   the southern Gulf of Mexico, is the best preserved of the three large
   multi-ring basins in the terrestrial record. The crater structure is
   characterized by a semi-circular concentric ring pattern, marking the
   crater basin, peak ring, terrace zone and basement uplift. Analysis of a
   grid of 19 seismic reflection profiles using seismic attributes, marker
   horizons, contour surfaces and 3-D views is used to investigate the
   stratigraphy of the central zone. We used interactive software and
   routine applications to map the impact breccias, breccia-carbonate
   contact and post-impact carbonates. Four horizons marked by
   high-amplitude reflectors representing high-impedance contrasts were
   identified and laterally correlated in the seismic images. Complex trace
   attribute analysis was applied for petrophysical characterization.
   Surface contour maps of base and top of stratigraphic packages were
   constructed, which mapped the impactites and post- and pre-impact
   carbonate stratigraphy. Basin floor, marked by the contact between the
   impact breccias and overlying carbonates is shown by laterally
   discontinuous high-amplitude reflectors. Discontinuous scattered
   reflectors interpreted as the upper breccias beneath the crater floor,
   have an average thickness of similar to 300msm. The Paleogene
   sedimentary units are characterized by multiple reflectors with lateral
   continuity, which contrast with the seismic response of underlying
   breccias. The basal Paleocene sediments follow the basin floor relief.
   Upwards in the section, the carbonate strata are characterized by
   horizontal reflectors, which are interrupted by a regional unconformity.
   Onlap/downlap packages over the unconformity record a period of sea
   level change.},
Publisher = {UNIV BARCELONA},
Address = {INST CIENCIES TERRA JAUME ALMERA-CSIC, LLUIS SOLE I SABARIS S-N,
   BARCELONA, E-08028, SPAIN},
Type = {Article},
Language = {English},
Affiliation = {Urrutia-Fucugauchi, J (Corresponding Author), Univ Nacl Autonoma Mexico, Inst Geofis, Dept Geomagnetismo \& Explorac, Programa Univ Perforac Oceanos \& Continentes, Ciudad Univ, Mexico City 04510, DF, Mexico.
   Canales-Garcia, I, Univ Nacl Autonoma Mexico, Posgrad Ciencias Mary \& Limnol, Ciudad Univ, Mexico City 04510, DF, Mexico.
   Urrutia-Fucugauchi, J., Univ Nacl Autonoma Mexico, Inst Geofis, Dept Geomagnetismo \& Explorac, Programa Univ Perforac Oceanos \& Continentes, Ciudad Univ, Mexico City 04510, DF, Mexico.
   Aguayo-Camargo, E., Univ Nacl Autonoma Mexico, Dept Geol, Fac Ingn, Ciudad Univ, Mexico City 04510, DF, Mexico.},
DOI = {10.1344/GeologicaActa2018.16.2.6},
ISSN = {1695-6133},
EISSN = {1696-5728},
Keywords = {Chicxulub Crater; Structure; Stratigraphy; Seismic attributes; Yucatan
   Platform; Gulf of Mexico},
Keywords-Plus = {IMPACT CRATER; BOREHOLE YAXCOPOIL-1; MAYA BLOCK; GRAVITY; ROCKS; SIZE;
   CONSTRAINTS; EMPLACEMENT; EXTINCTION; CARBONATES},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geology},
Author-Email = {juf@geofisica.unam.mx},
Affiliations = {Universidad Nacional Autonoma de Mexico; Universidad Nacional Autonoma
   de Mexico; Universidad Nacional Autonoma de Mexico},
Funding-Acknowledgement = {CONACYT scholarship; UNAM PAPIIT grant {[}IG-101115]},
Funding-Text = {Critical insightful comments by Gabriela Fernandez-Viejo, David Snyder,
   L. Perez-Cruz, the anonymous journal reviewers and section editor Puy
   Ayarza have been useful in revising the manuscript and are gratefully
   acknowledged. The study is based on the seismic data acquired by the
   Chicxulub Seismic Experiment (University of Texas at Austin Open-data
   repository). The Experiment was conducted as part of a joint project of
   University of Texas at Austin, the Imperial College Cambridge University
   and the Universidad Nacional Autonoma de Mexico (UNAM). We thank I.
   Dominguez-Trejo, L. Gonzalez-Mendoza, A. de J. Mendoza-Martinez, M.A.
   Diaz and M. Marca for their assistance. Thanks also to the Postgraduate
   course in Marine Science and Limnology at the UNAM. This study forms
   part of the Chicxulub Crater Research Program and UNAM Program for
   Continental and Ocean Drilling. Partial economic support for the study
   has been provided by a CONACYT scholarship to I. Canales-Garcia and the
   UNAM PAPIIT IG-101115 grant.},
Number-of-Cited-References = {62},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {13},
Journal-ISO = {Geol. Acta},
Doc-Delivery-Number = {GK3VO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000436077500006},
DA = {2024-01-15},
}

@article{ WOS:000453227400042,
Author = {Nishi, Katsuki and Shiokawa, Kazuo and Glassmeier, Karl-Heinz and Mieth,
   Johannes Z. D.},
Title = {Statistical Study of Phase Relationship Between Magnetic and Plasma
   Pressures in the Near-Earth Nightside Magnetosphere Using the THEMIS-E
   Satellite},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2018},
Volume = {123},
Number = {11},
Pages = {9517-9531},
Month = {NOV},
Abstract = {Distributions of plasma and magnetic pressures are the basic information
   to investigate macroscopic dynamics of the Earth's magnetosphere.
   Several studies have been made on magnetic and plasma pressures and
   macroscopic plasma instabilities in the magnetosphere. However,
   correlation between magnetic and plasma pressure variations has not been
   statistically investigated. In this paper, we analyze the statistical
   characteristics of the phase relationships between variations of
   magnetic and plasma pressures at frequencies of 4-15 mHz using 2 years
   of the THEMIS-E satellite data in the nightside magnetosphere. Spectral
   peaks with coherence greater than 0.85 between magnetic and plasma
   pressures for 1-hr time segments were selected. The average occurrence
   rates of the phase relationships are antiphase (within +/- 10 degrees
   from 180 degrees), 39.75\%; in-phase (within +/- 10 degrees from 0
   degrees), 0.73\%; and other phases (10-170 degrees), 49.83\%. For the
   other-phase events, the phase differences are much closer to antiphase
   rather than to in-phase. Thus, we conclude that the two pressure
   variations tend to be antiphase. The antiphase and in-phase
   relationships are observed mainly at radial distances outside 8 R-E and
   inside 8 R-E, respectively. The high occurrence region of antiphase
   relationship is in the dawnside during magnetically quiet times and
   shifts to dusk side at active times defined as Dst < -10 nT. The
   occurrence rates of the phase relationships do not change significantly
   depending on the AE and Dst indices, plasma beta, and IMF-B-z. Based on
   these results, we discuss the correspondence between the phase
   relationships and the possible magnetohydrodynamic force balances that
   can produce these phase relationships.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Shiokawa, K (Corresponding Author), Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan.
   Nishi, Katsuki; Shiokawa, Kazuo, Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan.
   Glassmeier, Karl-Heinz; Mieth, Johannes Z. D., Tech Univ Carolo Wilhelmina Braunschweig, Inst Geophys \& Extraterrestr Phys, Braunschweig, Germany.},
DOI = {10.1029/2018JA025846},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords-Plus = {FINGER-LIKE STRUCTURES; WAVES; SHEET},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {shiokawa@nagoya-u.jp},
Affiliations = {Nagoya University; Braunschweig University of Technology},
ORCID-Numbers = {Nishi, Katsuki/0000-0003-4863-649X
   Glassmeier, Karl-Heinz/0000-0003-4327-5576},
Funding-Acknowledgement = {NASA {[}NAS5-02099]; German Ministry for Economy and Technology; German
   Center for Aviation and Space (DLR) {[}50 OC 0302]; KAKENHI by the Japan
   Society for the Promotion of Science {[}JP 15H05815, JP 16H06286]; Japan
   Society for the Promotion of Science},
Funding-Text = {We acknowledge NASA contract NAS5-02099 and V. Angelopoulos for the use
   of data from the THEMIS mission. Specifically, we thank C. W. Carlson
   and J. P. Mcfadden for use of ESA data; D. Larson for use of SST data;
   K. H. Glassmeier, U. Auster, and W. Baumjohann for the use of FGM data
   provided under the lead of the Technical University of Braunschweig and
   with financial support through the German Ministry for Economy and
   Technology and the German Center for Aviation and Space (DLR) under
   contract 50 OC 0302. THEMIS probes data are available through the open
   data repository at UC Berkeley at
   http://themis.ssl.berkeley.edu/index.shtml. We also acknowledge use of
   NASA/GSFC Space physics Data Facility OMNIWeb
   (http://omniweb.gsfc.nasa.gov) service, and OMNI data. This work was
   supported by KAKENHI grants JP 15H05815 and JP 16H06286 provided by the
   Japan Society for the Promotion of Science.},
Number-of-Cited-References = {26},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {7},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {HE3CC},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000453227400042},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000507649300001,
Author = {Chen, Qi and Ruedl, Christiane},
Title = {Obesity retunes turnover kinetics of tissue-resident macrophages in fat},
Journal = {JOURNAL OF LEUKOCYTE BIOLOGY},
Year = {2020},
Volume = {107},
Number = {5, SI},
Pages = {773-782},
Month = {MAY},
Abstract = {Adipose tissue-resident F4/80(hi) macrophages (ATMs) are the main
   leukocyte population found in the visceral adipose tissue (VAT). These
   macrophages comprise several phenotypically distinct subpopulations that
   rapidly shift in abundance during obesity-induced tissue remodeling.
   Here we used a fate-mapping approach in mouse models to determine the
   developmental origins and the differential turnover kinetics of ATMs in
   lean and obese adipose tissue. We found that in lean, murine VAT the
   majority of ATMs express T cell immunoglobulin and mucin domain
   containing 4 receptor (Tim-4), lack the expression of CCR2 and can be
   further subdivided based on their expression of MHC class II and CD11c.
   We showed that both embryonic-derived Tim-4(+)MHCII(low) and
   Tim-4(+)MHCII(+) ATM subsets are long-lived and only slowly replenished
   by monocytes over time. Only a minor Tim-4(-)MHCII(+)CD11c(+) ATM
   fraction expresses CCR2 and is short-lived. In response to high-fat
   induced VAT remodeling, the majority of Tim-4(+)MHCII(low) ATMs maintain
   their fetal identity as they are moderately displaced by monocytes.
   Conversely, Tim-4(+)MHCII(+) ATMs are quickly replaced in a
   CCR2-dependent manner by bone marrow-derived Tim-4(-)MHCII(+) ATMs that
   have significantly higher turnover rates than those in lean mice. In
   addition, during high-fat diet, the subpopulation of CD11c(+)
   macrophages invade the VAT with the fastest turnover kinetics of all
   three ATM subpopulations. Our results suggest that ATM subpopulation
   frequency is controlled by the VAT microenvironment and that
   obesity-induced tissue remodeling renders some of the ATM niches
   accessible and available for rapid monocyte replenishment. Specialized
   monocyte-derived macrophages, which are rapidly recruited may be
   contributing to control the excess of adipocyte-released lipids produced
   during obesity.},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Ruedl, C (Corresponding Author), Nanyang Technol Univ, Sch Biol Sci, 60 Nanyang Dr, Singapore 637551, Singapore.
   Chen, Qi; Ruedl, Christiane, Nanyang Technol Univ, Sch Biol Sci, 60 Nanyang Dr, Singapore 637551, Singapore.},
DOI = {10.1002/JLB.1MA1219-275R},
EarlyAccessDate = {JAN 2020},
ISSN = {0741-5400},
EISSN = {1938-3673},
Keywords = {adipose tissue; fate mapping; long-lived; monocytes; replenishment; turn
   over},
Keywords-Plus = {MONOCYTES; MICROGLIA; REVEALS; ORIGIN; CELLS},
Research-Areas = {Cell Biology; Hematology; Immunology},
Web-of-Science-Categories  = {Cell Biology; Hematology; Immunology},
Author-Email = {Ruedl@ntu.edu.sg},
Affiliations = {Nanyang Technological University \& National Institute of Education
   (NIE) Singapore; Nanyang Technological University},
Funding-Acknowledgement = {Ministry of Education Tier2 grants {[}MOE2016-T2-1-012,
   MOE2018-T2-2-016]},
Funding-Text = {The authors thank Monika Tetlak for mouse management, Sheng Jianpeng for
   microglia isolation, and Insight Editing London for proofreading the
   manuscript prior to submission. This work was supported by Ministry of
   Education Tier2 grants awarded to C.R. (grant numbers: MOE2016-T2-1-012
   and MOE2018-T2-2-016). Original flow cytometry data are deposited in the
   NTU Open Access Data Repository DR-NTU.},
Number-of-Cited-References = {37},
Times-Cited = {14},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Leukoc. Biol.},
Doc-Delivery-Number = {LI2GZ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000507649300001},
DA = {2024-01-15},
}

@article{ WOS:000626823600001,
Author = {Habbouche, Houssem and Benkedjouh, Tarak and Zerhouni, Noureddine},
Title = {Intelligent prognostics of bearings based on bidirectional long
   short-term memory and wavelet packet decomposition},
Journal = {INTERNATIONAL JOURNAL OF ADVANCED MANUFACTURING TECHNOLOGY},
Year = {2021},
Volume = {114},
Number = {1-2},
Pages = {145-157},
Month = {MAY},
Abstract = {Bearing is one of the most sensitive components widely used in rotary
   machines and main cause for unexpected breakdown in rotating machinery.
   Bearing failure can lead to a lengthy downtime of the machine.
   Accurately predicting the damage trend of bearing is essential for
   planning maintenance, avoiding machine shutdowns and improving systems
   reliability. To reduce the maintenance cost of machine downtime, it is
   desirable to perform fault prognostics to enable predictive health
   management for bearings. This paper proposes a new data-driven approach
   for bearing prognostics based on wavelet packets decomposition and
   bidirectional long short-term memory, for preprocessing and tracking
   degradation process to estimate the remaining useful life. The proposed
   approach has two steps. The first step is to detect bearing's
   degradation process by learning the historical data and the second step
   is to predict the remaining useful life with the aid of a degradation
   model. The proposed approach is validated by bearing's life data
   obtained from a run-to-failure experiment. Results show that the
   proposed approach can detect the bearing degradation process
   successfully and predict the remaining useful life.},
Publisher = {SPRINGER LONDON LTD},
Address = {236 GRAYS INN RD, 6TH FLOOR, LONDON WC1X 8HL, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Benkedjouh, T (Corresponding Author), Ecole Mil Polytech, Mech Struct Lab, Algiers 16046, Algeria.
   Habbouche, Houssem; Benkedjouh, Tarak, Ecole Mil Polytech, Mech Struct Lab, Algiers 16046, Algeria.
   Zerhouni, Noureddine, UTBM, FEMTO ST Inst, UMR CNRS 6174,ENSMM, Automat Control \& Micromechatron Syst Dept,UFC, 24 Rue Alain Savary, F-25000 Besancon, France.},
DOI = {10.1007/s00170-021-06814-z},
EarlyAccessDate = {MAR 2021},
ISSN = {0268-3768},
EISSN = {1433-3015},
Keywords = {Bearings; Prognostics; Wavelet packet decomposition; Bidirectional long
   short-term memory; Remaining useful life},
Keywords-Plus = {USEFUL LIFE ESTIMATION; NEURAL-NETWORKS; MACHINE},
Research-Areas = {Automation \& Control Systems; Engineering},
Web-of-Science-Categories  = {Automation \& Control Systems; Engineering, Manufacturing},
Author-Email = {Houssemecanique@gmail.com
   bktarek@gmail.com
   noureddine.zerhouni@ens2m.fr},
Affiliations = {Ecole Military Polytechnic; Universite de Technologie de
   Belfort-Montbeliard (UTBM); Universite de Franche-Comte; Centre National
   de la Recherche Scientifique (CNRS); CNRS - Institute for Engineering \&
   Systems Sciences (INSIS)},
ResearcherID-Numbers = {HABBOUCHE, Houssem/AAE-7792-2022
   BENKEDJOUH, Tarak/S-6800-2019
   },
ORCID-Numbers = {HABBOUCHE, Houssem/0000-0003-0012-0769
   Benkedjouh, Tarak/0000-0002-0447-9106},
Funding-Acknowledgement = {research division of the polytechnic school},
Funding-Text = {This study was completed in the Mechanical Structures laboratory of the
   Polytechnic School of Algeria by the contribution of all authors, and
   with financial support from the research division of the polytechnic
   school. The authors would like to thank the University of Cincinnati for
   bearing dataset, IMS, NASA Ames Prognostics Data Repository, Rexnord
   Technical Services (2007), U.S.A, for providing free and open access to
   the bearing data sheet from their website {[}28].},
Number-of-Cited-References = {53},
Times-Cited = {9},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {50},
Journal-ISO = {Int. J. Adv. Manuf. Technol.},
Doc-Delivery-Number = {RN3PV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000626823600001},
DA = {2024-01-15},
}

@article{ WOS:001085733400005,
Author = {Britten, Richard A. and Fesshaye, Arriyam and Tidmore, Alyssa and Liu,
   Aiyi and Blackwell, Ashley A.},
Title = {Loss of Cognitive Flexibility Practice Effects in Female Rats Exposed to
   Simulated Space Radiation},
Journal = {RADIATION RESEARCH},
Year = {2023},
Volume = {200},
Number = {3},
Pages = {256-265},
Month = {SEP},
Abstract = {During the planned missions to Mars, astronauts will be faced with many
   potential health hazards including prolonged exposure to space
   radiation. Ground-based studies have shown that exposure to space
   radiation impairs the performance of male rats in cognitive flexibility
   tasks which involve processes that are essential to rapidly and
   efficiently adapting to different situations. However, there is
   presently a paucity of information on the effects of space radiation on
   cognitive flexibility in female rodents. This study has determined the
   impact that exposure to a low (10 cGy) dose of ions from the simplified
   5-ion galactic cosmic ray simulation
   {[}https://www.bnl.gov/nsrl/userguide/SimGCRSim.php (07/2023)] (GCRSim)
   beam or 250 MeV/n He-4 ions has on the ability of female Wistar rats to
   perform in constrained {[}attentional set shifting (ATSET)] and
   unconstrained cognitive flexibility (UCFlex) tasks. Female rats exposed
   to GCRSim exhibited multiple decrements in ATSET performance. Firstly,
   GCRSim exposure impaired performance in the compound discrimination (CD)
   stage of the ATSET task. While the ability of rats to identify the
   rewarded cue was not compromised, the time the rats required to do so
   significantly increased. Secondly, both He-4 and GCRSim exposure reduced
   the ability of rats to reach criterion in the compound discrimination
   reversal (CDR) stage. Approximately 20\% of the irradiated rats were
   unable to complete the CDR task; furthermore, the irradiated rats that
   did reach criterion took more attempts to do so than did the
   sham-treated animals. Radiation exposure also altered the magnitude
   and/or nature of practice effects. A comparison of performance metrics
   from the pre-screen and post-exposure ATSET task revealed that while the
   sham-treated rats completed the post-exposure CD stage of the ATSET task
   in 30\% less time than for completion of the pre-screen ATSET task, the
   irradiated rats took 30-50\% longer to do so. Similarly, while
   sham-treated rats completed the CDR stage in similar to 10\% fewer
   attempts in the post-exposure task compared to the pre-screen task, in
   contrast, the He-4- and GCRSim-exposed cohorts took more (similar to
   2-fold) attempts to reach criterion in the post-exposure task than in
   the pre-screen task. In conclusion, this study demonstrates that female
   rats are susceptible to radiation-induced loss of performance in the
   constrained ATSET cognitive flexibility task. Moreover, exposure to
   radiation leads to multiple performance decrements, including loss of
   practice effects, an increase in anterograde interference and reduced
   ability or unwillingness to switch attention. Should similar effects
   occur in humans, astronauts may have a compromised ability to perform
   complex tasks. (c) 2023 by Radiation Research Society},
Publisher = {RADIATION RESEARCH SOC},
Address = {810 E TENTH STREET, LAWRENCE, KS 66044 USA},
Type = {Article},
Language = {English},
Affiliation = {Britten, RA (Corresponding Author), Eastern Virginia Med Sch, EVMS Radiat Oncol, 700W Olney Rd,Lewis Hall, Norfolk, VA 23507 USA.
   Britten, Richard A.; Fesshaye, Arriyam; Tidmore, Alyssa; Liu, Aiyi; Blackwell, Ashley A., EVMS Radiat Oncol, Norfolk, VA 23507 USA.
   Britten, Richard A., EVMS Microbiol \& Mol Cell Biol, Norfolk, VA 23507 USA.
   Britten, Richard A.; Blackwell, Ashley A., Eastern Virginia Med Sch, Ctr Integrat Neurosci \& Inflammatory Dis, Norfolk, VA 23507 USA.},
DOI = {10.1667/RADE-22-00196.1},
ISSN = {0033-7587},
EISSN = {1938-5404},
Keywords-Plus = {SET-SHIFTING PERFORMANCE; LONG-TERM POTENTIATION; SYNAPTIC PLASTICITY;
   NEURONAL OUTPUT; PARTICLES; CGY; HIPPOCAMPUS; AGE},
Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Biophysics; Radiology,
   Nuclear Medicine \& Medical Imaging},
Web-of-Science-Categories  = {Biology; Biophysics; Radiology, Nuclear Medicine \& Medical Imaging},
Author-Email = {brittera@evms.edu},
Affiliations = {Eastern Virginia Medical School},
Funding-Acknowledgement = {NASA {[}NNX14AE73G]},
Funding-Text = {This work was funded by NASA grant support NNX14AE73G (RAB). The authors
   are indebted to Dr. Adam Rusek and his staff for their help with the
   irradiation of the rats at Brookhaven National Laboratories. This study
   would not have been possible without their help. Open Science: The
   individualized performance data will be available within NASA's Open
   Science Data Repository and in Supplemental Data file.},
Number-of-Cited-References = {58},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Radiat. Res.},
Doc-Delivery-Number = {U6FG1},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001085733400005},
DA = {2024-01-15},
}

@article{ WOS:000558452100011,
Author = {Yang, Yuanxuan and Heppenstall, Alison and Turner, Andy and Comber,
   Alexis},
Title = {Using graph structural information about flows to enhance short-term
   demand prediction in bike-sharing systems},
Journal = {COMPUTERS ENVIRONMENT AND URBAN SYSTEMS},
Year = {2020},
Volume = {83},
Month = {SEP},
Abstract = {Short-term demand prediction is important for managing transportation
   infrastructure, particularly in times of disruption, or around new
   developments. Many bike-sharing schemes face the challenges of managing
   service provision and bike fleet rebalancing due to the ``tidal
   flows{''} of travel and use. For them, it is crucial to have precise
   predictions of travel demand at a fine spatiotemporal granularities.
   Despite recent advances in machine learning approaches (e.g. deep neural
   networks) and in short-term traffic demand predictions, relatively few
   studies have examined this issue using a feature engineering approach to
   inform model selection. This research extracts novel time-lagged
   variables describing graph structures and flow interactions from
   real-world bike usage datasets, including graph node Out-strength,
   In-strength, Out-degree, In-degree and PageRank. These are used as
   inputs to different machine learning algorithms to predict short-term
   bike demand. The results of the experiments indicate the graph-based
   attributes to be more important in demand prediction than more commonly
   used meteorological information. The results from the different machine
   learning approaches (XGBoost, MLP, LSTM) improve when time-lagged graph
   information is included. Deep neural networks were found to be better
   able to handle the sequences of the time-lagged graph variables than
   other approaches, resulting in more accurate forecasting. Thus
   incorporating graph-based features can improve understanding and
   modelling of demand patterns in urban areas, supporting bike-sharing
   schemes and promoting sustainable transport. The proposed approach can
   be extended into many existing models using spatial data and can be
   readily transferred to other applications for predicting dynamics in
   mass transit systems. A number of limitations and areas of further work
   are discussed.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Yang, YX (Corresponding Author), Univ Leeds, Sch Geog, Leeds LS2 9JT, W Yorkshire, England.
   Yang, YX (Corresponding Author), Univ Liverpool, Dept Geog \& Planning, Liverpool, Merseyside, England.
   Yang, Yuanxuan; Heppenstall, Alison; Turner, Andy; Comber, Alexis, Univ Leeds, Sch Geog, Leeds LS2 9JT, W Yorkshire, England.
   Yang, Yuanxuan, Univ Liverpool, Dept Geog \& Planning, Liverpool, Merseyside, England.},
DOI = {10.1016/j.compenvurbsys.2020.101521},
Article-Number = {101521},
ISSN = {0198-9715},
EISSN = {1873-7587},
Keywords = {Bike-sharing; Traffic prediction; Graph theory; Urban dynamics;
   Sustainable transport},
Keywords-Plus = {PUBLIC-TRANSIT; TRAFFIC FLOW; TIME-SERIES; PATTERNS; NETWORK},
Research-Areas = {Computer Science; Engineering; Environmental Sciences \& Ecology;
   Geography; Operations Research \& Management Science; Public
   Administration},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Engineering,
   Environmental; Environmental Studies; Geography; Operations Research \&
   Management Science; Regional \& Urban Planning},
Author-Email = {yuanxuan.yang@liverpool.ac.uk},
Affiliations = {University of Leeds; University of Liverpool},
ResearcherID-Numbers = {Heppenstall, Alison/N-4354-2015
   },
ORCID-Numbers = {Heppenstall, Alison/0000-0002-0663-3437
   Turner, Andy/0000-0002-6098-6313
   Yang, Yuanxuan/0000-0002-7970-2544},
Funding-Acknowledgement = {University of Leeds and Chinese Scholarship Council {[}201606420071];
   Natural Environment Research Council {[}NE/S009124/1]; Economic and
   Social Research Council Alan Turing research fellowship
   {[}ES/R007918/1]; NERC {[}NE/S009124/1] Funding Source: UKRI},
Funding-Text = {This study is supported and funded by University of Leeds and Chinese
   Scholarship Council (201606420071), the Natural Environment Research
   Council (NE/S009124/1) and the Economic and Social Research Council Alan
   Turing research fellowship (ES/R007918/1). Part of the data and codes
   used in this analysis are openly available from University of Leeds open
   access data repository (https://doi.org/10.5518/851). We thank the
   anonymous reviewers whose comments and suggestions helped improve and
   clarify this manuscript.},
Number-of-Cited-References = {65},
Times-Cited = {43},
Usage-Count-Last-180-days = {10},
Usage-Count-Since-2013 = {70},
Journal-ISO = {Comput. Environ. Urban Syst.},
Doc-Delivery-Number = {MY5IY},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000558452100011},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000488657500021,
Author = {Yang, Yuanxuan and Heppenstall, Alison and Turner, Andy and Comber,
   Alexis},
Title = {A spatiotemporal and graph-based analysis of dockless bike sharing
   patterns to understand urban flows over the last mile},
Journal = {COMPUTERS ENVIRONMENT AND URBAN SYSTEMS},
Year = {2019},
Volume = {77},
Month = {SEP},
Abstract = {The recent emergence of dockless bike sharing systems has resulted in
   new patterns of urban transport. Users can begin and end trips from
   their origin and destination locations rather than docking stations.
   Analysis of changes in the spatiotemporal availability of such bikes has
   the ability to provide insights into urban dynamics at a finer
   granularity than is possible through analysis of travel card or
   dock-based bike scheme data. This study analyses dockless bike sharing
   in Nanchang, China over a period when a new metro line came into
   operation. It uses spatial statistics and graph-based approaches to
   quantify changes in travel behaviours and generates previously
   unobtainable insights about urban flow structures. Geostatistical
   analyses support understanding of large-scale changes in spatiotemporal
   travel behaviours and graph-based approaches allow changes in local
   travel flows between individual locations to be quantified and
   characterized. The results show how the new metro service boosted nearby
   bike demand, but with considerable spatial variation, and changed the
   spatiotemporal patterns of bike travel behaviour. The analysis also
   quantifies the evolution of travel flow structures, indicating the
   resilience of dockless bike schemes and their ability to adapt to
   changes in travel behaviours. More widely, this study demonstrates how
   an enhanced understanding of urban dynamics over the ``last-mile{''} is
   supported by the analyses of dockless bike data. These allow changes in
   local spatiotemporal interdependencies between different transport
   systems to be evaluated, and support spatially detailed urban and
   transport planning. A number of areas of further work are identified to
   better to understand interdependencies between different transit system
   components.},
Publisher = {ELSEVIER SCI LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Yang, YX (Corresponding Author), Univ Leeds, Sch Geog, Leeds LS2 9JT, W Yorkshire, England.
   Yang, Yuanxuan; Heppenstall, Alison; Turner, Andy; Comber, Alexis, Univ Leeds, Sch Geog, Leeds LS2 9JT, W Yorkshire, England.},
DOI = {10.1016/j.compenvurbsys.2019.101361},
Article-Number = {101361},
ISSN = {0198-9715},
EISSN = {1873-7587},
Keywords = {Goddess bikes; Urban dynamics; Spatial analysis; Graph structure;
   Transportation},
Keywords-Plus = {MOBILITY PATTERNS; PUBLIC-TRANSIT; RIDERSHIP; IMPACTS; USAGE; CITY},
Research-Areas = {Computer Science; Engineering; Environmental Sciences \& Ecology;
   Geography; Operations Research \& Management Science; Public
   Administration},
Web-of-Science-Categories  = {Computer Science, Interdisciplinary Applications; Engineering,
   Environmental; Environmental Studies; Geography; Operations Research \&
   Management Science; Regional \& Urban Planning},
Author-Email = {gyyy@leeds.ac.uk},
Affiliations = {University of Leeds},
ResearcherID-Numbers = {Heppenstall, Alison/N-4354-2015
   },
ORCID-Numbers = {Heppenstall, Alison/0000-0002-0663-3437
   Turner, Andy/0000-0002-6098-6313
   Yang, Yuanxuan/0000-0002-7970-2544},
Funding-Acknowledgement = {University of Leeds and Chinese Scholarship Council {[}201606420071];
   Natural Environment Research Council {[}NE/S009124/1]; Economic and
   Social Research Council Alan Turing research fellowship
   {[}ES/R007918/1]; ESRC {[}ES/S007164/1, ES/R007918/1, ES/L011891/1]
   Funding Source: UKRI; NERC {[}NE/S009124/1] Funding Source: UKRI},
Funding-Text = {This study is supported and funded by University of Leeds and Chinese
   Scholarship Council (201606420071), the Natural Environment Research
   Council (NE/S009124/1) and the Economic and Social Research Council Alan
   Turing research fellowship (ES/R007918/1). We thank the anonymous
   reviewers whose comments and suggestions helped improve and clarify this
   manuscript. Part of the data and codes used in this analysis are openly
   available from University of Leeds open access data repository
   (https://doi.org/10.5518/619).},
Number-of-Cited-References = {44},
Times-Cited = {89},
Usage-Count-Last-180-days = {12},
Usage-Count-Since-2013 = {134},
Journal-ISO = {Comput. Environ. Urban Syst.},
Doc-Delivery-Number = {JB6EN},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000488657500021},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000576620600002,
Author = {Morris, V, R. and Rampe, E. B. and Vaniman, D. T. and Christoffersen, R.
   and Yen, A. S. and Morrison, S. M. and Ming, D. W. and Achilles, C. N.
   and Fraeman, A. A. and Le, L. and Tu, V. M. and Ott, J. P. and Treiman,
   A. H. and Hogancamp, V, J. and Graff, T. G. and Adams, M. and Hamilton,
   J. C. and Mertzman, S. A. and Bristow, T. F. and Blake, D. F. and
   Castle, N. and Chipera, S. J. and Craig, I, P. and Des Marais, D. J. and
   Downs, G. and Downs, R. T. and Hazen, R. M. and Morookian, J-M and
   Thorpe, M.},
Title = {Hydrothermal Precipitation of Sanidine (Adularia) Having Full Al,Si
   Structural Disorder and Specular Hematite at Maunakea Volcano (Hawai'i)
   and at Gale Crater (Mars)},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-PLANETS},
Year = {2020},
Volume = {125},
Number = {9},
Month = {SEP},
Abstract = {Hydrothermal high sanidine and specular hematite are found within
   ferric-rich and gray-colored cemented basaltic breccia occurring within
   horizontal, weathering-resistant strata exposed in an erosional gully of
   the Pu'u Poliahu cinder cone in the summit region of Maunakea volcano
   (Hawai'i). The cone was extensively altered by hydrothermal,
   acid-sulfate fluids at temperatures up to similar to 400 degrees C, and,
   within strata, plagioclase was removed by dissolution from progenitor
   Hawaiitic basalt, and sanidine and hematite were precipitated. Fe2O3T
   concentration and Fe3+/ n-ary sumation Fe redox state are similar to 12
   wt.\% and similar to 0.4 for progenitor basalt and 46-60 wt.\% and
   similar to 1.0 for cemented breccias, respectively, implying open-system
   alteration and oxic precipitation. Hydrothermal high sanidine (adularia)
   is characterized by full Al,Si structural disorder and monoclinic
   unit-cell (Rietveld refinement):a = 8.563(19) angstrom, b = 13.040(6)
   angstrom, c = 7.169(4) angstrom, beta = 116.02(10)degrees, andV =
   719.4(19) angstrom(3). Hematite (structure confirmed by Rietveld
   refinement) is the predominant Fe-bearing phase detected. Coarse size
   fractions of powdered hematite-rich breccia (500-1000 mu m) are dark and
   spectrally neutral at visible wavelengths, confirming specular hematite,
   and SEM images show platy to polyhedral hematite morphologies with
   longest dimensions >10 mu m. Smectite and 10-angstrom phyllosilicate,
   both chemically dominated by Mg as octahedral cation, are additional
   diagenetic hydrothermal alteration products. By analogy and as a working
   hypothesis, high sanidine (Kimberly formation) and specular hematite
   (Mt. Sharp group at Hartmann's Valley and Vera Rubin ridge) at Gale
   crater are interpreted as diagenetic alteration products of Martian
   basaltic material by hydrothermal processes.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Morris, RV (Corresponding Author), NASA, Johnson Space Ctr, Houston, TX 77058 USA.
   Morris, R., V; Rampe, E. B.; Ming, D. W.; Thorpe, M., NASA, Johnson Space Ctr, Houston, TX 77058 USA.
   Vaniman, D. T.; Craig, P., I, Planetary Sci Inst, Tucson, AZ USA.
   Christoffersen, R.; Le, L.; Tu, V. M.; Hogancamp, J., V; Graff, T. G., NASA, Jacobs, Johnson Space Ctr, Houston, TX USA.
   Yen, A. S.; Fraeman, A. A.; Morookian, J-M, CALTECH, Jet Prop Lab, Pasadena, CA USA.
   Morrison, S. M.; Hazen, R. M., Carnegie Inst Sci, Washington, DC 20005 USA.
   Achilles, C. N., NASA, Goddard Space Flight Ctr, Greenbelt, MD USA.
   Ott, J. P., Harvard Univ, Cambridge, MA 02138 USA.
   Treiman, A. H., USRA, Lunar \& Planetary Inst, Houston, TX USA.
   Adams, M.; Hamilton, J. C., Univ Hawaii, Dept Phys \& Astron, Hilo, HI 96720 USA.
   Mertzman, S. A., Franklin \& Marshall Coll, Lancaster, PA 17604 USA.
   Bristow, T. F.; Blake, D. F.; Castle, N.; Des Marais, D. J., NASA, Ames Res Ctr, Moffett Field, CA 94035 USA.
   Chipera, S. J., CHK Energy, Oklahoma City, OK USA.
   Downs, G.; Downs, R. T., Univ Arizona, Dept Geosci, Tucson, AZ 85721 USA.},
DOI = {10.1029/2019JE006324},
Article-Number = {e2019JE006324},
ISSN = {2169-9097},
EISSN = {2169-9100},
Keywords-Plus = {HOSTED EPITHERMAL DEPOSITS; UNIT-CELL PARAMETERS; X-RAY-DIFFRACTION;
   ALKALI FELDSPARS; CRYSTAL-STRUCTURE; ACID-SULFATE; STRUCTURE REFINEMENT;
   OPTICAL-PROPERTIES; SOLID-SOLUTION; K-FELDSPARS},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {richard.v.morris@nasa.gov},
Affiliations = {National Aeronautics \& Space Administration (NASA); National
   Aeronautics \& Space Administration (NASA); California Institute of
   Technology; National Aeronautics \& Space Administration (NASA); NASA
   Jet Propulsion Laboratory (JPL); Carnegie Institution for Science;
   National Aeronautics \& Space Administration (NASA); NASA Goddard Space
   Flight Center; Harvard University; University of Hawaii System;
   University Hawaii Hilo; Franklin \& Marshall College; National
   Aeronautics \& Space Administration (NASA); NASA Ames Research Center;
   University of Arizona},
ORCID-Numbers = {Morris, Richard/0000-0003-1413-4002
   Morrison, Shaunna/0000-0002-1712-8057},
Funding-Acknowledgement = {NASA Mars Science Laboratory Project; NASA Johnson Space Center; Jet
   Propulsion Laboratory, California Institute of Technology; NASA},
Funding-Text = {Maunakea field work and samples were obtained in partnership with the
   Pacific International Space Center for Exploration Systems with
   permission from the Office of Mauna Kea Management, the Mauna Kea
   Management Board, Board of Land and Natural Resources, and the cultural
   Hawaiian Kahu KMauna Council. We are greatly appreciative of the shared
   knowledge and sustained efforts of these organizations in the protection
   and preservation of the unique cultural and natural resources of
   Maunakea. The manuscript benefitted from careful reading and comments by
   anonymous reviewers and from discussion with John Grotzinger. Supporting
   Information consists of two spreadsheets available for downloading from
   the Open Data Repository
   (https://odr.io/Morrisetal2020\_JGR\_2019JE006324): (a) direct download
   of unit-cell parameters for sanidine and hematite
   (https://odr.io/view/downloadfile/60903) and (b) direct download of
   hematite spectra and spectral parameters
   (https://odr.io/view/downloadfile/60902) and direct download of Maunakea
   XRD patterns (https://odr.io/view/downloadfile/60904). Support for this
   work by the NASA Mars Science Laboratory Project, the NASA Johnson Space
   Center, and the Jet Propulsion Laboratory, California Institute of
   Technology (under a contract with NASA) is acknowledged.},
Number-of-Cited-References = {106},
Times-Cited = {12},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {11},
Journal-ISO = {J. Geophys. Res.-Planets},
Doc-Delivery-Number = {NY8GD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000576620600002},
OA = {hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000295389000001,
Author = {Brach, Anthony R. and Boufford, David E.},
Title = {WHY ARE WE STILL PRODUCING PAPER FLORAS?},
Journal = {ANNALS OF THE MISSOURI BOTANICAL GARDEN},
Year = {2011},
Volume = {98},
Number = {3},
Pages = {297-300},
Abstract = {Advances in online resources and electronic publication provide the
   sciences with tools to revolutionize education and research (e.g.,
   cataloging, data archiving and access, and identification). Older
   journals and monographs are being scanned and increasingly posted online
   quickly by book scanning projects, although even for new issues, there
   can be a ``moving wall{''} or lag time (e.g., BioOne and JSTOR). Some
   scientific disciplines are providing the public with pre-print access to
   articles in digital libraries, while manuscript availability in other
   disciplines, such as nomenclatural botany, is often delayed until the
   time of print publication. Within botany, taxonomic treatments should be
   provided online at all stages of preparation and revision (in certain
   cases following initial editing). Now, many published floras can be
   browsed and searched online (e.g., Flora of North America, Jepson
   Manual, Flora of Australia). The Flora of China Project provides
   treatments at all stages, online, prior to printing of volumes. Because
   of this visibility, the Flora of China Web site regularly receives
   questions from the general public and helpful review comments from
   botanists worldwide. With pressing issues of cataloging biodiversily,
   conservation, and sustainable use of resources, botanists are challenged
   to prepare and revise online treatments, including interactive
   identification keys and images, for a worldwide audience of students and
   researchers.},
Publisher = {MISSOURI BOTANICAL GARDEN},
Address = {2345 TOWER GROVE AVENUE, ST LOUIS, MO 63110 USA},
Type = {Article},
Language = {English},
Affiliation = {Brach, AR (Corresponding Author), Harvard Univ Herbaria, Missouri Bot Garden, 22 Divin Ave, Cambridge, MA 02138 USA.
   Brach, Anthony R., Harvard Univ Herbaria, Missouri Bot Garden, Cambridge, MA 02138 USA.},
DOI = {10.3417/2010035},
ISSN = {0026-6493},
Keywords = {digital floras; digital libraries; electronic publication; Flora of
   China; interactive identification keys; species-id.net},
Keywords-Plus = {IDENTIFICATION; FUTURE; PLANTS},
Research-Areas = {Plant Sciences},
Web-of-Science-Categories  = {Plant Sciences},
Author-Email = {brach@oeb.harvard.edu},
Affiliations = {Harvard University; Missouri Botanical Gardens},
Funding-Acknowledgement = {U.S. National Science Foundation {[}BSR-8906215, BSR-9201378, DEB
   9626806, DEB 0072682, DEB 0343439, DEB-0514279, DEB-0722217,
   DEB-0810237, DEB-0813935]},
Funding-Text = {We are thankful to numerous individuals for their discussions of this
   topic. We thank Flora of China Project contributors, editors, and
   reviewers for allowing their draft and revised treatments to be posted
   online. We are grateful to Hong Cui (University of Arizona) for using
   the Flora of China treatments as a test of the MARTT system and for
   providing the Greenstone Digital Library, Gregor Hagedorn (Julius
   Kuhn-institute, Germany) for creating the open data repository on
   species-id.net, Hong Song (St. Louis University) for incorporating
   floristic volumes into eFloras.org, Myriam Fica (MO) for assistance in
   updating the data, and Anne Marie Countie (Harvard University) and Chris
   Freeland (MO) for their support of servers at the Harvard University
   Herbaria and Missouri Botanical Garden, respectively. We are thankful
   for helpful comments by the editor Victoria Hollowell (MO) and three
   reviewers: Tom Rosatti (JEPS), Peter F. Stevens (MO), and Mike Dallwitz
   (Giralang, Australia). Support of the U.S. National Science Foundation
   (BSR-8906215, BSR-9201378, DEB 9626806, DEB 0072682, DEB 0343439,
   DEB-0514279, DEB-0722217, DEB-0810237, and DEB-0813935) for the Flora of
   China Project is gratefully acknowledged.},
Number-of-Cited-References = {30},
Times-Cited = {8},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {19},
Journal-ISO = {Ann. Mo. Bot. Gard.},
Doc-Delivery-Number = {826XN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000295389000001},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000486046800010,
Author = {Koumakis, Nick and Brown, Aidan T. and Arlt, Jochen and Griffiths,
   Samuel E. and Martinez, Vincent A. and Poon, Wilson C. K.},
Title = {Dynamic optical rectification and delivery of active particles},
Journal = {SOFT MATTER},
Year = {2019},
Volume = {15},
Number = {35},
Pages = {7026-7032},
Month = {SEP 21},
Abstract = {We use moving light patterns to control the motion of Escherichia coli
   bacteria whose motility is photo-activated. Varying the pattern speed
   controls the magnitude and direction of the bacterial flux, and
   therefore the accumulation of cells in up- and down-stream reservoirs.
   We validate our results with two-dimensional simulations and a
   1-dimensional analytic model, and use these to explore parameter space.
   We find that cell accumulation is controlled by a competition between
   directed flux and undirected, stochastic transport. Our results point to
   a number of design principles for using moving light patterns and
   light-activated micro-swimmers in a range of practical applications.},
Publisher = {ROYAL SOC CHEMISTRY},
Address = {THOMAS GRAHAM HOUSE, SCIENCE PARK, MILTON RD, CAMBRIDGE CB4 0WF, CAMBS,
   ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Koumakis, N (Corresponding Author), Univ Edinburgh, SUPA, James Clerk Maxwell Bldg,Peter Guthrie Tait Rd, Edinburgh EH9 3FD, Midlothian, Scotland.
   Koumakis, Nick; Brown, Aidan T.; Arlt, Jochen; Griffiths, Samuel E.; Martinez, Vincent A.; Poon, Wilson C. K., Univ Edinburgh, SUPA, James Clerk Maxwell Bldg,Peter Guthrie Tait Rd, Edinburgh EH9 3FD, Midlothian, Scotland.
   Koumakis, Nick; Brown, Aidan T.; Arlt, Jochen; Griffiths, Samuel E.; Martinez, Vincent A.; Poon, Wilson C. K., Univ Edinburgh, Sch Phys \& Astron, James Clerk Maxwell Bldg,Peter Guthrie Tait Rd, Edinburgh EH9 3FD, Midlothian, Scotland.},
DOI = {10.1039/c9sm00799g},
ISSN = {1744-683X},
EISSN = {1744-6848},
Keywords-Plus = {ESCHERICHIA-COLI; MOTILITY},
Research-Areas = {Chemistry; Materials Science; Physics; Polymer Science},
Web-of-Science-Categories  = {Chemistry, Physical; Materials Science, Multidisciplinary; Physics,
   Multidisciplinary; Polymer Science},
Author-Email = {nick.koumakis@ed.ac.uk},
Affiliations = {University of Edinburgh; University of Edinburgh},
ResearcherID-Numbers = {Arlt, Jochen/B-7435-2009
   Brown, Aidan T/M-4897-2017
   Poon, Wilson C K/B-5960-2013
   Martinez, Vincent A/D-2906-2009},
ORCID-Numbers = {Arlt, Jochen/0000-0002-4152-5896
   Brown, Aidan T/0000-0002-6898-4021
   Poon, Wilson C K/0000-0003-0760-7940
   Martinez, Vincent A/0000-0003-2395-5929},
Funding-Acknowledgement = {EU {[}654688]; UK EPSRC {[}EP/J007404/1, EP/S001255/1]; ERC
   {[}ERC-2013-AdG 340877-PHYSAP]; EPSRC studentship; Marie Curie Actions
   (MSCA) {[}654688] Funding Source: Marie Curie Actions (MSCA); BBSRC
   {[}BB/R012415/1] Funding Source: UKRI; EPSRC {[}1861845, EP/J007404/1,
   EP/S001255/1] Funding Source: UKRI},
Funding-Text = {We thank Teun Vissers and Mike Cates for discussions. NK was part-funded
   by the EU (H2020-MSCA-IF-2014, ActiDoC No. 654688). AB received funding
   from UK EPSRC (EP/S001255/1). All except SEG received funding from UK
   EPSRC (EP/J007404/1) and ERC (Advanced Grant ERC-2013-AdG
   340877-PHYSAP). SEG held an EPSRC studentship. The raw microscopy images
   are available on the University of Edinburgh DataShare open access data
   repository at https://doi.org/10.7488/ds/2603.},
Number-of-Cited-References = {21},
Times-Cited = {7},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Soft Matter},
Doc-Delivery-Number = {IX9YJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000486046800010},
OA = {Green Published, Green Accepted, Green Submitted, hybrid},
DA = {2024-01-15},
}

@article{ WOS:001021723100001,
Author = {Baillargeon, Keith R. and Brooks, Jessica C. and Miljanic, Philip R. and
   Mace, Charles R.},
Title = {Patterned Dried Blood Spot Cards for the Improved Sampling of Whole
   Blood},
Journal = {ACS MEASUREMENT SCIENCE AU},
Year = {2021},
Volume = {2},
Number = {1},
Pages = {31-38},
Month = {SEP 17},
Abstract = {Dried blood spot (DBS) cards perform many functions for sampling blood
   that is intended for subsequent laboratory analysis, which include: (i)
   obviating the need for a phlebotomist by using fingersticks, (ii)
   enhancing the stability of analytes at ambient or elevated environmental
   conditions, and (iii) simplifying the transportation of samples without
   a cold chain. However, a significant drawback of standard DBS cards is
   the potential for sampling bias due to unrestricted filling caused by
   the hematocrit of blood, which often limits quantitative or reproducible
   measurements. Alternative microsampling technologies have minimized or
   eliminated this bias by restricting blood distribution, but these
   approaches deviate from clinical protocols and present a barrier to
   broad adoption. Herein, we describe a patterned dried blood spot (pDBS)
   card that uses wax barriers to control the flow and restrict the
   distribution of blood to provide enhanced sampling. These patterned
   cards reproducibly fill four replicate extraction zones independent of
   the hematocrit effect. We demonstrate a 3-fold improvement in accuracy
   for the quantitation of hemoglobin using pDBS cards compared to
   unpatterned cards. Patterned cards also facilitate the near quantitative
   recovery (ca. 95\%) of sodium with no evidence of a statistically
   significant difference between dried and liquid blood samples.
   Similarly, the recovery of select amino acids was conserved in
   comparison to a recent report with improved intercard precision. We
   anticipate that this approach presents a viable method for preparing and
   storing samples of blood in limited resource settings while maintaining
   current clinical protocols for processing and analyzing dried blood
   spots.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Mace, CR (Corresponding Author), Tufts Univ, Dept Chem, Medford, MA 02155 USA.
   Mace, CR (Corresponding Author), Tufts Univ, Lab Living Devices, Medford, MA 02155 USA.
   Baillargeon, Keith R.; Brooks, Jessica C.; Miljanic, Philip R.; Mace, Charles R., Tufts Univ, Dept Chem, Medford, MA 02155 USA.
   Baillargeon, Keith R.; Brooks, Jessica C.; Miljanic, Philip R.; Mace, Charles R., Tufts Univ, Lab Living Devices, Medford, MA 02155 USA.},
DOI = {10.1021/acsmeasuresciau.1c00031},
EISSN = {2694-250X},
Keywords = {paper microfluidics; paper analytical devices; \& mu;PAD; driedblood
   spot cards; point-of-care; bioanalysis; hematology},
Keywords-Plus = {HEMATOCRIT; FABRICATION; ASSAYS},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Analytical},
Author-Email = {charles.mace@tufts.edu},
Affiliations = {Tufts University; Tufts University},
Funding-Acknowledgement = {Bill amp; Melinda Gates Foundation {[}OPP1182231]; grant conditions of
   the Foundation; Tufts University Office of the Vice Provost for Research
   (OVPR) Research and Scholarship Strategic Plan (RSSP); Tufts Launchpad
   Accelerator program; Bill and Melinda Gates Foundation {[}OPP1182231]
   Funding Source: Bill and Melinda Gates Foundation},
Funding-Text = {This work was supported, in whole or in part, by the Bill \& Melinda
   Gates Foundation {[}grant number OPP1182231]. Under the grant conditions
   of the Foundation, a Creative Commons Attribution 4.0 Generic License
   has already been assigned to the Author Accepted Manuscript version that
   might arise from this submission. In accordance with the Bill \& Melinda
   Gates Foundation Open Access Policy, all data found in the figures and
   tables of this manuscript has been uploaded to Zenodo, an open access
   data repository, at a persistent DOI
   (https://doi.org/10.5281/zenodo.5371557). The project was additionally
   supported by the Tufts University Office of the Vice Provost for
   Research (OVPR) Research and Scholarship Strategic Plan (RSSP) and by
   the Tufts Launchpad Accelerator program.},
Number-of-Cited-References = {47},
Times-Cited = {11},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {ACS Meas. Sci. Au},
Doc-Delivery-Number = {L2PF6},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001021723100001},
OA = {Green Published, Green Submitted, gold},
DA = {2024-01-15},
}

@article{ WOS:000549789600001,
Author = {Kariyawasam, Kasun D. and Middleton, Campbell R. and Madabhushi, Gopal
   and Haigh, Stuart K. and Talbot, James P.},
Title = {Assessment of bridge natural frequency as an indicator of scour using
   centrifuge modelling},
Journal = {JOURNAL OF CIVIL STRUCTURAL HEALTH MONITORING},
Year = {2020},
Volume = {10},
Number = {5},
Pages = {861-881},
Month = {NOV},
Abstract = {One of the most prevalent causes of bridge failure around the world is
   ``scour{''}-the gradual erosion of soil around a bridge foundation due
   to fast-flowing water. A reliable technique for monitoring scour would
   help bridge engineers take timely countermeasures to safeguard against
   failure. Although vibration-based techniques for monitoring structural
   damage have had limited success, primarily due to insufficient
   sensitivity, these have tended to focus on the detection of local
   damage. High natural frequency sensitivity has recently been reported
   for scour damage. Previous experiments to investigate this have been
   limited as a result of the cost of full-scale testing and the fact that
   scaled-down soil-structure models tested outside a centrifuge do not
   adequately simulate full-scale behaviour. This paper describes the
   development of what is believed to be the first-ever centrifuge-testing
   programme to establish the sensitivity of bridge natural frequency to
   scour. A 1/60 scale model of a two-span integral bridge with 15 m spans
   was tested at varying levels of scour. For the fundamental mode of
   vibration, these tests found up to a 40\% variation in natural frequency
   for 30\% loss of embedment. Models of three other types of foundation,
   which represent a shallow pad foundation, a deep pile bent and a deep
   monopile, were also tested in the centrifuge at different scour levels.
   The shallow foundation model showed lower frequency sensitivity to scour
   than the deep foundation models. Another important finding is that the
   frequency sensitivity to ``global scour{''} is slightly higher than the
   sensitivity to ``local scour{''}, for all foundation types. The level of
   frequency sensitivity (3.1-44\% per scour depth equivalent to 30\% of
   embedment of scour) detected in this experiment demonstrates the
   potential for using natural frequency as an indicator of both local and
   global scour of bridges, particularly those with deep foundations.},
Publisher = {SPRINGER HEIDELBERG},
Address = {TIERGARTENSTRASSE 17, D-69121 HEIDELBERG, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Kariyawasam, KD (Corresponding Author), Univ Cambridge, Dept Engn, Cambridge, England.
   Kariyawasam, Kasun D.; Middleton, Campbell R.; Madabhushi, Gopal; Haigh, Stuart K.; Talbot, James P., Univ Cambridge, Dept Engn, Cambridge, England.},
DOI = {10.1007/s13349-020-00420-5},
EarlyAccessDate = {JUL 2020},
ISSN = {2190-5452},
EISSN = {2190-5479},
Keywords = {Vibration-based scour monitoring; Bridge scour; Natural frequency;
   Centrifuge modelling; Integral bridge},
Keywords-Plus = {IDENTIFICATION; PIER},
Research-Areas = {Engineering},
Web-of-Science-Categories  = {Engineering, Civil},
Author-Email = {kdk26@cam.ac.uk
   crm11@cam.ac.uk
   mspg1@cam.ac.uk
   skh20@cam.ac.uk
   jpt1000@cam.ac.uk},
Affiliations = {University of Cambridge},
Funding-Acknowledgement = {Cambridge Centre for Smart Infrastructure and Construction (Innovate UK)
   {[}920035]; Cambridge Centre for Smart Infrastructure and Construction
   (EPSRC) {[}EP/N021614/1]; Laing O'Rourke Centre for Construction
   Engineering and Technology; Gates Cambridge Trust {[}OPP1144]; EPSRC
   {[}EP/L010917/1] Funding Source: UKRI},
Funding-Text = {We are grateful to the Cambridge Centre for Smart Infrastructure and
   Construction (Innovate UK Grant reference number 920035 and EPSRC Grant
   no EP/N021614/1), and the Laing O'Rourke Centre for Construction
   Engineering and Technology, for the funding provided for this
   experimental programme. The PhD funding provided by the Gates Cambridge
   Trust, founded by the Bill and Melinda Gates Foundation (Grant number
   OPP1144), is also gratefully appreciated. The valuable support provided
   by Tom Williams during the planning stage of this project is
   acknowledged. The research facilities provided by the Schofield Centre
   are gratefully acknowledged. We would like to acknowledge the initial
   development of the air hammer set-up by Peter Kirkwood and the
   piezoelectric actuator set-up by Jing Dong for testing monopiles. We
   thank Deryck Chan and Jad Boksmati for the valuable guidance provided to
   run the centrifuge test. We would also like to thank Geoff Eichhorn,
   Ahmed Alagha and Thejesh Garala for their guidance during the model
   preparation. Finally, thanks to Scofield Centre senor technicians
   Kristian Pether, Chris McGinnie, Mark Smith, John Chandler and David
   Layfield for their assistance at different stages of the experiment.
   Data supporting this paper is available from the University of Cambridge
   Open Data repository {[}58].},
Number-of-Cited-References = {58},
Times-Cited = {21},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {21},
Journal-ISO = {J. Civ. Struct. Health Monit.},
Doc-Delivery-Number = {NV4MG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000549789600001},
OA = {hybrid, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000955688700001,
Author = {Zhao, Qian and Chen, Qiang and van Dam, Tonie and She, Yawen and Wu,
   Weiwei},
Title = {The vertical velocity field of the Tibetan Plateau and its surrounding
   areas derived from GPS and surface mass loading models},
Journal = {EARTH AND PLANETARY SCIENCE LETTERS},
Year = {2023},
Volume = {609},
Month = {MAY 1},
Abstract = {Obtaining a precise velocity field of the Earth's surface is critical
   for probing Earth's tectonic movements. In this contribution we
   construct a precise vertical velocity field with high-spatial resolution
   for the Tibetan Plateau (TP) and its surrounding areas using both 113
   continuous and 969 campaign GPS time series over the period 2008 to
   2019. Specifically, we compared the statistical distribution of residual
   continuous GPS time series to find the optimal regional surface mass
   loading (SML) models. The optimal modeled nontectonic displacements were
   used to correct these campaign GPS time series to reduce their scatter
   and accordingly improve the precision of the uplift rate estimates. The
   results showed that we could reduce the root mean square (RMS) on the
   vertical coordinate time series by more than 75\% of the campaign GPS
   stations. We computed and removed vertical deformation due to horizontal
   strain rates obtained from GPS time series, and discussed dynamic
   sources (mantle dynamic topography, isostatic adjustment, and flexural
   loading) that drive the residual vertical tectonic motion. The study
   presents the most recent surface kinematic constraints for comprehending
   the dynamic sources of tectonic uplift or subsidence between and within
   tectonic units. Plain Language Summary: Movements of the Tibetan Plateau
   (TP) have a profound impact on adjacent areas. We collected all
   available GPS data to determine a precise vertical velocity field with
   high-spatial resolution. We make use of optimal surface mass loading
   (SML) models to improve estimation accuracy of campaign GPS stations,
   including an estimate of the vertical movement caused by the horizontal
   tectonic motions. We combine geological and geophysical data with our
   vertical velocity field to understand the dynamic sources of uplift or
   subsidence between and within tectonic units of the TP. (c) 2023
   Elsevier B.V. All rights reserved.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Zhao, Q (Corresponding Author), China Earthquake Adm, Inst Earthquake Forecasting, Beijing 100036, Peoples R China.
   Zhao, Qian; She, Yawen; Wu, Weiwei, China Earthquake Adm, Inst Earthquake Forecasting, Beijing 100036, Peoples R China.
   Chen, Qiang, Univ Luxembourg, Fac Sci Technol \& Med, Esch Sur Alzette, Luxembourg.
   van Dam, Tonie, Univ Utah, Coll Mines \& Earth Sci, Dept Geol \& Geophys, Salt Lake City, UT USA.},
DOI = {10.1016/j.epsl.2023.118107},
EarlyAccessDate = {MAR 2023},
Article-Number = {118107},
ISSN = {0012-821X},
EISSN = {1385-013X},
Keywords = {Tibet Plateau; nontectonic deformation; surface mass loading; vertical
   GPS velocity; dynamic source},
Keywords-Plus = {CRUSTAL DEFORMATION; BENEATH EASTERN; SEA-LEVEL; COLLISION; GRACE;
   LITHOSPHERE; TECTONICS; ISOSTASY; GRAVITY; MARGIN},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {qianzhao411@126.com},
Affiliations = {China Earthquake Administration; University of Luxembourg; Utah System
   of Higher Education; University of Utah},
ResearcherID-Numbers = {van Dam, Tonie/G-5822-2014
   },
ORCID-Numbers = {van Dam, Tonie/0000-0001-6562-6563
   She, Yawen/0000-0003-3666-2666},
Funding-Acknowledgement = {Crustal Move- ment Observation Network of China; National Natural
   Science Foundation of China {[}41974012]; National Key R\&D Program of
   China {[}2018YFC1503503]},
Funding-Text = {We thank NASA, GFZ and EOST for providing the surface mass loading
   products, and the GPS data support from the Crustal Movement Observation
   Network of China (CMONOC) which is managed by the National Earthquake
   Data Center. This work was supported by the National Natural Science
   Foundation of China (41974012) and the National Key R \& D Program of
   China (2018YFC1503503) . The GNSS time series and GNSS-derived
   velocities and related results are available from the open -access data
   repository through the link https://doi .org/10 .5281/zenodo .7672699.},
Number-of-Cited-References = {55},
Times-Cited = {1},
Usage-Count-Last-180-days = {14},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Earth Planet. Sci. Lett.},
Doc-Delivery-Number = {A5RK0},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000955688700001},
DA = {2024-01-15},
}

@article{ WOS:000387312000017,
Author = {Savre, Julien and Percival, James and Herzog, Michael and Pain, Chris},
Title = {Two-Dimensional Evaluation of ATHAM-Fluidity, a Nonhydrostatic
   Atmospheric Model Using Mixed Continuous/Discontinuous Finite Elements
   and Anisotropic Grid Optimization},
Journal = {MONTHLY WEATHER REVIEW},
Year = {2016},
Volume = {144},
Number = {11},
Pages = {4349-4372},
Month = {NOV},
Abstract = {This paper presents the first attempt to apply the compressible
   nonhydrostatic Active Tracer High-Resolution Atmospheric Model-Fluidity
   (ATHAM-Fluidity) solver to a series of idealized atmospheric test cases.
   ATHAM-Fluidity uses a hybrid finite-element discretization where
   pressure is solved on a continuous second-order grid while momentum and
   scalars are computed on a first-order discontinuous grid (also known as
   P-1DG - P-2). ATHAM-Fluidity operates on two-and three-dimensional
   unstructured meshes, using triangular or tetrahedral elements,
   respectively, with the possibility to employ an anisotropic mesh
   optimization algorithm for automatic grid refinement and coarsening
   during run time. The solver is evaluated using two-dimensional-only dry
   idealized test cases covering a wide range of atmospheric applications.
   The first three cases, representative of atmospheric convection, reveal
   the ability of ATHAM-Fluidity to accurately simulate the evolution of
   large-scale flow features in neutral atmospheres at rest. Grid
   convergence without adaptivity as well as the performances of the
   Hermite-Weighted Essentially Nonoscillatory (Hermite-WENO) slope limiter
   are discussed. These cases are also used to test the grid optimization
   algorithm implemented in ATHAM-Fluidity. Adaptivity can result in up toa
   sixfold decrease in computational time and a fivefold decrease in total
   element number for the same finest resolution. However, substantial
   discrepancies are found between the uniform and adapted grid results,
   thus suggesting the necessity to improve the reliability of the
   approach. In the last three cases, corresponding to atmospheric gravity
   waves with and without orography, the model ability to capture the
   amplitude and propagation of weak stationary waves is demonstrated. This
   work constitutes the first step toward the development of a new
   comprehensive limited area atmospheric model.},
Publisher = {AMER METEOROLOGICAL SOC},
Address = {45 BEACON ST, BOSTON, MA 02108-3693 USA},
Type = {Article},
Language = {English},
Affiliation = {Savre, J (Corresponding Author), Univ Cambridge, Dept Geog, Downing Pl, Cambridge CB2 3EN, England.
   Savre, Julien; Herzog, Michael, Univ Cambridge, Dept Geog, Downing Pl, Cambridge CB2 3EN, England.
   Percival, James; Pain, Chris, Imperial Coll London, Royal Sch Mines, Dept Earth Sci \& Engn, London, England.},
DOI = {10.1175/MWR-D-15-0398.1},
ISSN = {0027-0644},
EISSN = {1520-0493},
Keywords-Plus = {DISCONTINUOUS GALERKIN METHODS; SHALLOW-WATER EQUATIONS; SPECTRAL
   ELEMENT; DYNAMICAL CORE; SCHEME; SIMULATION; MESOSCALE; FLOWS;
   FORMULATION; ADAPTIVITY},
Research-Areas = {Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Meteorology \& Atmospheric Sciences},
Author-Email = {js2176@cam.ac.uk},
Affiliations = {University of Cambridge; Imperial College London},
ResearcherID-Numbers = {Herzog, Michael/B-4722-2010
   },
ORCID-Numbers = {Herzog, Michael/0000-0003-3903-573X
   Pain, Christopher/0000-0003-4194-2590},
Funding-Acknowledgement = {European Union {[}603663]; EPSRC {[}EP/N010221/1, EP/P013198/1] Funding
   Source: UKRI; NERC {[}NE/N013727/1, NE/H002987/1] Funding Source: UKRI;
   Engineering and Physical Sciences Research Council {[}EP/P013198/1,
   EP/N010221/1] Funding Source: researchfish; Natural Environment Research
   Council {[}NE/N013727/1, NE/H002987/1] Funding Source: researchfish},
Funding-Text = {This research has received funding from the European Union Seventh
   Framework Program (FP7/2007-2013) under Grant Agreement 603663 for the
   research project PEARL(Preparing for Extreme And Rare events in coastaL
   regions). C. Pain and J. Percival would also like to acknowledge the
   EPSRC multiphase program grant MEMPHIS. Finally, the authors thank the
   editor, Hilary Weller, as well as three anonymous reviewers for their
   valuable comments and suggestions. All data presented in this manuscript
   are freely available through the open-access online data repository
   Zenodo (https://zenodo.org).},
Number-of-Cited-References = {59},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Mon. Weather Rev.},
Doc-Delivery-Number = {EB4AS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000387312000017},
OA = {Green Submitted, hybrid, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000455713600013,
Author = {Horst, Nicole K. and Jupp, Bianca and Roberts, Angela C. and Robbins,
   Trevor W.},
Title = {D2 receptors and cognitive flexibility in marmosets: tri-phasic
   dose-response effects of intra-striatal quinpirole on serial reversal
   performance},
Journal = {NEUROPSYCHOPHARMACOLOGY},
Year = {2019},
Volume = {44},
Number = {3},
Pages = {564-571},
Month = {FEB},
Abstract = {Behavioral flexibility, which allows organisms to adapt their actions in
   response to environmental changes, is impaired in a number of
   neuropsychiatric conditions, including obsessive-compulsive disorder and
   addiction. Studies in human subjects and monkeys have reported
   correlations between individual differences in dopamine D2-type receptor
   (D2R) levels in the caudate nucleus and performance in a discrimination
   reversal task, in which established contingent relationships between
   abstract stimuli and rewards (or punishments) are reversed. Global
   genetic deletion of the D2R in mice disrupts reversal performance,
   indicating a likely causal role for this receptor in supporting flexible
   behaviors. To directly examine the specific role of caudate D2-type
   receptors in reversal performance, the D2/3/4R agonist quinpirole was
   infused via chronic indwelling cannulae into the medial caudate of male
   and female marmoset monkeys performing a touchscreen-based serial
   discrimination reversal task. Given prior evidence for dose-dependent
   effects of quinpirole and other dopaminergic drugs, a full dose-response
   curve was established. Individually, marmosets displayed marked
   differences in behavioral sensitivity to specific doses of intra-caudate
   quinpirole. Collectively, they exhibited a behaviorally specific
   bi-phasic deficit in reversal learning, being consistently impaired at
   both relatively low and high doses of quinpirole. However, intermediate
   doses of intra-caudate quinpirole produced significant improvement in
   reversal performance. These data support previous human and monkey
   neuroimaging studies by providing causal evidence of a U-shaped function
   describing how dopamine modulates cognitive flexibility in the primate
   striatum.},
Publisher = {NATURE PUBLISHING GROUP},
Address = {MACMILLAN BUILDING, 4 CRINAN ST, LONDON N1 9XW, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Horst, NK (Corresponding Author), Univ Cambridge, Dept Psychol, Cambridge CB2 3EB, England.
   Horst, NK (Corresponding Author), Univ Cambridge, Behav \& Clin Neurosci Inst, Downing St, Cambridge CB2 3EB, England.
   Horst, Nicole K.; Jupp, Bianca; Robbins, Trevor W., Univ Cambridge, Dept Psychol, Cambridge CB2 3EB, England.
   Horst, Nicole K.; Jupp, Bianca; Roberts, Angela C.; Robbins, Trevor W., Univ Cambridge, Behav \& Clin Neurosci Inst, Downing St, Cambridge CB2 3EB, England.
   Roberts, Angela C., Univ Cambridge, Dept Physiol Dev \& Neurosci, Downing St, Cambridge CB2 3DY, England.},
DOI = {10.1038/s41386-018-0272-9},
ISSN = {0893-133X},
EISSN = {1740-634X},
Keywords-Plus = {OBSESSIVE-COMPULSIVE DISORDER; PREFRONTAL CORTEX; ORBITOFRONTAL CORTEX;
   DORSOMEDIAL STRIATUM; PARKINSONS-DISEASE; ATTENTIONAL-SET; DOPAMINE;
   LESIONS; DISCRIMINATION; SENSITIVITY},
Research-Areas = {Neurosciences \& Neurology; Pharmacology \& Pharmacy; Psychiatry},
Web-of-Science-Categories  = {Neurosciences; Pharmacology \& Pharmacy; Psychiatry},
Author-Email = {nh382@cam.ac.uk},
Affiliations = {University of Cambridge; University of Cambridge; University of
   Cambridge},
ResearcherID-Numbers = {Robbins, Trevor William/A-7551-2008
   Roberts, Angela C/C-1313-2012
   },
ORCID-Numbers = {Roberts, Angela C/0000-0003-2873-157X
   Robbins, Trevor/0000-0003-0642-5977
   Jupp, Bianca/0000-0002-9163-9170},
Funding-Acknowledgement = {Wellcome Trust {[}104631/Z/14/Z, MRC-G1000183]; Medical Research
   Council; Wellcome Trust; MRC {[}G1000183, MR/J012084/1] Funding Source:
   UKRI},
Funding-Text = {All data supporting this publication are freely available at
   https://doi.org/10.17863/CAM.32242 as part of the University of
   Cambridge data repository. This work was supported by a Wellcome Trust
   Senior Investigator Award (104631/Z/14/Z to T.W.R.) and conducted within
   the University of Cambridge Behavioural and Clinical Neuroscience
   Institute, supported by a joint award from the Medical Research Council
   and the Wellcome Trust (MRC-G1000183). Funding to pay the open access
   publication charges for this article was provided by the Wellcome Trust.},
Number-of-Cited-References = {56},
Times-Cited = {22},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {Neuropsychopharmacology},
Doc-Delivery-Number = {HH4RV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000455713600013},
OA = {hybrid, Green Accepted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000949573100014,
Author = {Komeazi, Abolfazl and Kaviani, Ayoub and Ruempker, Georg},
Title = {Mantle Anisotropy in NW Namibia From XKS Splitting: Effects of
   Asthenospheric Flow, Lithospheric Structures, and Magmatic Underplating},
Journal = {GEOPHYSICAL RESEARCH LETTERS},
Year = {2023},
Volume = {50},
Number = {3},
Month = {FEB 16},
Abstract = {The presence of the Etendeka flood basalts in northwestern Namibia is
   taken as evidence for the activity of the Tristan da Cunha mantle plume
   during the continental breakup between Africa and South America. We
   investigate seismic anisotropy beneath NW Namibia by splitting analysis
   of core-refracted teleseismic shear waves (XKS phases) to probe mantle
   flow and lithospheric deformation related to the tectonic history of the
   region. We present the results of the joint splitting analysis of XKS
   data collected from 34 onshore stations and 12 ocean-bottom
   seismometers. The fast polarization directions (FPDs) are consistent
   with a model that combines the effects of lithospheric deformation and
   large-scale mantle flow due to the NE motion of the African plate. The
   dominantly NNW-SSE-oriented FPDs in the northern part are likely caused
   by shallow lithospheric structures. Our observations do not show any
   strong evidence of a pervasive effect of the Tristan da Cunha mantle
   plume.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Komeazi, A (Corresponding Author), Goethe Univ Frankfurt, Inst Geosci, Frankfurt, Germany.
   Komeazi, Abolfazl; Kaviani, Ayoub; Ruempker, Georg, Goethe Univ Frankfurt, Inst Geosci, Frankfurt, Germany.
   Ruempker, Georg, Frankfurt Inst Adv Studies, Frankfurt, Germany.},
DOI = {10.1029/2022GL102119},
ISSN = {0094-8276},
EISSN = {1944-8007},
Keywords = {seismic anisotropy; Tristan da Cunha mantle plume; Namibia; lithospheric
   shearing; continental breakup; shear wave splitting},
Keywords-Plus = {SEISMIC ANISOTROPY; WALVIS RIDGE; KAOKO BELT; BENEATH; PLUME;
   DEFORMATION; HOTSPOT; EVOLUTION; VOLCANISM; JUNCTION},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {komeazi@geophysik.uni-frankfurt.de},
Affiliations = {Goethe University Frankfurt},
ResearcherID-Numbers = {Kaviani, Ayoub/ACP-5435-2022
   },
ORCID-Numbers = {Kaviani, Ayoub/0000-0001-5818-1594
   Komeazi, Abolfazl/0000-0003-2411-9770
   Rumpker, Georg/0000-0002-5348-9888},
Funding-Acknowledgement = {International Federation of Digital Seismograph Networks; Projekt DEAL},
Funding-Text = {We thank the GEOFON data repository of Deutsches Geoforschungszentrum
   Potsdam (GFZ) for providing data from the temporary seismic networks XC
   and 6A, and the IRIS Data Management Center for the data from the
   permanent station TSUM (Albuquerque Seismo-logical Laboratory/USGS,
   2014, Global Seismograph Network (GSN-IRIS/USGS) {[}Data Set].
   International Federation of Digital Seismograph Networks.
   https://doi.org/10.7914/SN/IU). We would also like to thank Lucia
   Margheriti and an anonymous reviewer for helpful suggestions and
   constructive comments on an earlier version of the manuscript. Open
   Access funding enabled and organized by Projekt DEAL.},
Number-of-Cited-References = {60},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Geophys. Res. Lett.},
Doc-Delivery-Number = {9X1ZT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000949573100014},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000460902200070,
Author = {Kapsch, Marie-Luise and Skific, Natasa and Graversen, Rune G. and
   Tjernstrom, Michael and Francis, Jennifer A.},
Title = {Summers with low Arctic sea ice linked to persistence of spring
   atmospheric circulation patterns},
Journal = {CLIMATE DYNAMICS},
Year = {2019},
Volume = {52},
Number = {3-4},
Pages = {2497-2512},
Month = {FEB},
Abstract = {The declining trend of Arctic September sea ice constitutes a
   significant change in the Arctic climate system. Large year-to-year
   variations are superimposed on this sea-ice trend, with the largest
   variability observed in the eastern Arctic Ocean. Knowledge of the
   processes important for this variability may lead to an improved
   understanding of seasonal and long-term changes. Previous studies
   suggest that transport of heat and moisture into the Arctic during
   spring enhances downward surface longwave radiation, thereby controlling
   the annual melt onset, setting the stage for the September ice minimum.
   In agreement with these studies, we find that years with a low September
   sea-ice concentration (SIC) are characterized by more persistent periods
   in spring with enhanced energy flux to the surface in forms of net
   longwave radiation plus turbulent fluxes, compared to years with a high
   SIC. Two main atmospheric circulation patterns related to these episodes
   are identified: one resembles the so-called Arctic dipole anomaly that
   promotes transport of heat and moisture from the North Pacific, whereas
   the other is characterized by negative geopotential height anomalies
   over the Arctic, favoring cyclonic flow from Siberia and the Kara Sea
   into the eastern Arctic Ocean. However, differences between years with
   low and high September SIC appear not to be due to different spring
   circulation patterns; instead it is the persistence and intensity of
   processes associated with these patterns that distinguish the two groups
   of anomalous years: Years with low September SIC feature episodes that
   are consistently stronger and more persistent than years with high SIC.},
Publisher = {SPRINGER},
Address = {ONE NEW YORK PLAZA, SUITE 4600, NEW YORK, NY, UNITED STATES},
Type = {Article},
Language = {English},
Affiliation = {Kapsch, ML (Corresponding Author), Stockholm Univ, Dept Meteorol, S-10691 Stockholm, Sweden.
   Kapsch, ML (Corresponding Author), Stockholm Univ, Bolin Ctr Climate Res, S-10691 Stockholm, Sweden.
   Kapsch, ML (Corresponding Author), Max Planck Inst Meteorol, Bundesstr 53, D-20146 Hamburg, Germany.
   Kapsch, Marie-Luise; Tjernstrom, Michael, Stockholm Univ, Dept Meteorol, S-10691 Stockholm, Sweden.
   Kapsch, Marie-Luise; Tjernstrom, Michael, Stockholm Univ, Bolin Ctr Climate Res, S-10691 Stockholm, Sweden.
   Kapsch, Marie-Luise, Max Planck Inst Meteorol, Bundesstr 53, D-20146 Hamburg, Germany.
   Skific, Natasa; Francis, Jennifer A., Rutgers State Univ, Dept Marine \& Coastal Sci, 71 Dudley Rd, New Brunswick, NJ 08901 USA.
   Graversen, Rune G., Univ Tromso, Dept Phys \& Technol, Postbox 6050, N-9037 Tromso, Norway.},
DOI = {10.1007/s00382-018-4279-z},
ISSN = {0930-7575},
EISSN = {1432-0894},
Keywords = {Climate variability; Arctic sea ice; Self organizing maps (SOMs);
   Atmospheric circulation; Atmospheric energy transport},
Keywords-Plus = {SELF-ORGANIZING MAPS; MELT; TRANSPORT; PERFORMANCE; RECORD; MASS},
Research-Areas = {Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Meteorology \& Atmospheric Sciences},
Author-Email = {marie.kapsch@mpimet.mpg.de},
Affiliations = {Stockholm University; Stockholm University; Max Planck Society; Rutgers
   System; Rutgers New Brunswick; UiT The Arctic University of Tromso},
ResearcherID-Numbers = {Kapsch, Marie-Luise/AAI-7512-2020
   Tjernström, Michael/AAF-3481-2020
   Graversen, Rune G/C-3956-2016
   Francis, Jennifer/JPX-0349-2023
   },
ORCID-Numbers = {Kapsch, Marie-Luise/0000-0001-9551-5370
   Graversen, Rune/0000-0003-4899-553X},
Funding-Acknowledgement = {Max Planck Society; Swedish research council Formas through the ADSIMNOR
   project; NASA Grant {[}NNX14AH896]; Swedish e-Science Research Center
   (SeRC)},
Funding-Text = {Open access funding provided by Max Planck Society. The authors are
   grateful to the anonymous reviewers for their constructive comments and
   valuable suggestions, which helped to significantly improve the
   manuscript. The ERA-Interim data is provided by the ECMWF and was
   downloaded from the MARS data repository. The computations were
   performed on resources provided by the Swedish National Infrastructure
   for Computing (SNIC) at Linkoping University. MLK was funded by the
   Swedish research council Formas through the ADSIMNOR project. JAF and NS
   are supported by the NASA Grant NNX14AH896. MLK is also grateful for
   support from the Swedish e-Science Research Center (SeRC).},
Number-of-Cited-References = {42},
Times-Cited = {25},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Clim. Dyn.},
Doc-Delivery-Number = {HO4OM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000460902200070},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000359666000005,
Author = {Brookfield, Katherine and Fitzsimons, Claire and Scott, Iain and Mead,
   Gillian and Starr, John and Thin, Neil and Tinker, Anthea and Thompson,
   Catharine Ward},
Title = {The home as enabler of more active lifestyles among older people},
Journal = {BUILDING RESEARCH AND INFORMATION},
Year = {2015},
Volume = {43},
Number = {5, SI},
Pages = {616-630},
Month = {SEP 3},
Abstract = {Inactive lifestyles have negative health consequences, while time spent
   sedentary (sitting and lying) is related to morbidity and premature
   mortality. Older adults often form the most sedentary segment of the
   population. Much of this behaviour may be practised at home where this
   group can spend extended periods. Physical activity rates among older
   adults are particularly low. Even household physical activities can be
   beneficial for this group, while they can constitute much of an older
   person's total activity. Despite this context, the home's role in the
   active and sedentary behaviours of the older population appears
   critically understudied. Using interview and focus group data collected
   from 22 older adults (healthy volunteers, stroke survivors and people
   with dementia), this paper begins to address this issue. Aspects of the
   home that aid or impede a more active, less sedentary lifestyle are
   identified with three presenting particular capacity in this respect
   discussed: steps, space within the home, and the location and form of
   facilities, fixtures and fittings. The crucial role health status plays
   in structuring this capacity is identified. Simple design
   recommendations, devised to support older people to lead more active
   lives at home, are presented.},
Publisher = {ROUTLEDGE JOURNALS, TAYLOR \& FRANCIS LTD},
Address = {2-4 PARK SQUARE, MILTON PARK, ABINGDON OX14 4RN, OXON, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Brookfield, K (Corresponding Author), Univ Edinburgh, Edinburgh Coll Art, 74 Lauriston Pl,Hunter Bldg, Edinburgh EH3 9DF, Midlothian, Scotland.
   Brookfield, Katherine; Scott, Iain; Thompson, Catharine Ward, Univ Edinburgh, Edinburgh Coll Art, Edinburgh EH3 9DF, Midlothian, Scotland.
   Fitzsimons, Claire, Univ Edinburgh, Inst Sport Phys Educ \& Hlth Sci, Edinburgh EH8 8AQ, Midlothian, Scotland.
   Mead, Gillian, Univ Edinburgh, Royal Infirm Edinburgh, Edinburgh EH16 5NN, Midlothian, Scotland.
   Starr, John, Univ Edinburgh, Alzheimer Scotland Dementia Res Ctr, Edinburgh EH8 9JZ, Midlothian, Scotland.
   Thin, Neil, Univ Edinburgh, Sch Social \& Polit Sci, Edinburgh EH8 9LD, Midlothian, Scotland.
   Tinker, Anthea, Kings Coll London, Inst Gerontol, Dept Social Sci Hlth \& Med, London WC2R 2LS, England.},
DOI = {10.1080/09613218.2015.1045702},
ISSN = {0961-3218},
EISSN = {1466-4321},
Keywords = {active design; active living; age; built environment; design
   characteristics; home; housing; older adults; physical activity;
   sedentary behaviour},
Keywords-Plus = {INTENSITY PHYSICAL-ACTIVITY; SEDENTARY BEHAVIOR; ACTIVITY RESTRICTION;
   UNITED-STATES; TIME SPENT; COMMUNITY; ADULTS; HEALTH; DEMENTIA;
   ENVIRONMENT},
Research-Areas = {Construction \& Building Technology},
Web-of-Science-Categories  = {Construction \& Building Technology},
Author-Email = {katherine.brookfield@ed.ac.uk
   claire.fitzsimons@ed.ac.uk
   iain.scott@ed.ac.uk
   gillian.e.mead@ed.ac.uk
   jstarr@staffmail.ed.ac.uk
   n.thin@ed.ac.uk
   anthea.tinker@kcl.ac.uk
   c.ward-thompson@ed.ac.uk},
Affiliations = {University of Edinburgh; Edinburgh College of Art; University of
   Edinburgh; University of Edinburgh; Royal Infirmary of Edinburgh;
   University of Edinburgh; University of Edinburgh; University of London;
   King's College London},
ResearcherID-Numbers = {Ward Thompson, Catharine/JFA-9237-2023
   },
ORCID-Numbers = {Ward Thompson, Catharine/0000-0002-9563-0026
   Tinker, Anthea/0000-0002-0305-7198},
Funding-Acknowledgement = {Research Councils UK under the Lifelong Health and Wellbeing
   Cross-Council Programme {[}EP/K037404/1]; Engineering and Physical
   Sciences Research Council {[}EP/K037404/1] Funding Source: researchfish;
   EPSRC {[}EP/K037404/1] Funding Source: UKRI},
Funding-Text = {This work was supported by Research Councils UK under the Lifelong
   Health and Wellbeing Cross-Council Programme {[}grant reference number
   EP/K037404/1]. The raw data associated with this publication contain
   personal/sensitive information (interviews and focus groups with
   individuals) and cannot be released. At the end of the three-year
   project to which this publication relates an anonymised version of these
   data may be considered for deposit in the University of Edinburgh's
   open-access data repository Edinburgh DataShare. Raw data will be
   securely stored after the project in the proposed non-public Data Vault
   service that the university will offer researchers.},
Number-of-Cited-References = {94},
Times-Cited = {21},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {20},
Journal-ISO = {Build. Res. Informat.},
Doc-Delivery-Number = {CP1VX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000359666000005},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000462722700007,
Author = {Schuldt, Andreas and Ebeling, Anne and Kunz, Matthias and Staab, Michael
   and Guimaraes-Steinicke, Claudia and Bachmann, Doerte and Buchmann, Nina
   and Durka, Walter and Fichtner, Andreas and Fornoff, Felix and Haerdtle,
   Werner and Hertzog, Lionel R. and Klein, Alexandra-Maria and Roscher,
   Christiane and Schaller, Joerg and von Oheimb, Goddert and Weigelt,
   Alexandra and Weisser, Wolfgang and Wirth, Christian and Zhang, Jiayong
   and Bruelheide, Helge and Eisenhauer, Nico},
Title = {Multiple plant diversity components drive consumer communities across
   ecosystems},
Journal = {NATURE COMMUNICATIONS},
Year = {2019},
Volume = {10},
Month = {MAR 29},
Abstract = {Humans modify ecosystems and biodiversity worldwide, with negative
   consequences for ecosystem functioning. Promoting plant diversity is
   increasingly suggested as a mitigation strategy. However, our
   mechanistic understanding of how plant diversity affects the diversity
   of heterotrophic consumer communities remains limited. Here, we
   disentangle the relative importance of key components of plant diversity
   as drivers of herbivore, predator, and parasitoid species richness in
   experimental forests and grasslands. We find that plant species richness
   effects on consumer species richness are consistently positive and
   mediated by elevated structural and functional diversity of the plant
   communities. The importance of these diversity components differs across
   trophic levels and ecosystems, cautioning against ignoring the
   fundamental ecological complexity of biodiversity effects. Importantly,
   plant diversity effects on higher trophic-level species richness are in
   many cases mediated by modifications of consumer abundances. In light of
   recently reported drastic declines in insect abundances, our study
   identifies important pathways connecting plant diversity and consumer
   diversity across ecosystems.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Schuldt, A (Corresponding Author), German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany.
   Schuldt, A (Corresponding Author), Martin Luther Univ Halle Wittenberg, Inst Biol Geobot, Kirchtor 1, D-06108 Halle, Germany.
   Schuldt, A (Corresponding Author), Martin Luther Univ Halle Wittenberg, Bot Garden, Kirchtor 1, D-06108 Halle, Germany.
   Schuldt, A (Corresponding Author), Georg August Univ Gottingen, Fac Forest Sci, Forest Nat Conservat, Busgenweg 3, D-37077 Gottingen, Germany.
   Schuldt, Andreas; Durka, Walter; Roscher, Christiane; von Oheimb, Goddert; Weigelt, Alexandra; Wirth, Christian; Bruelheide, Helge; Eisenhauer, Nico, German Ctr Integrat Biodivers Res iDiv, Deutsch Pl 5e, D-04103 Leipzig, Germany.
   Schuldt, Andreas; Bruelheide, Helge, Martin Luther Univ Halle Wittenberg, Inst Biol Geobot, Kirchtor 1, D-06108 Halle, Germany.
   Schuldt, Andreas; Bruelheide, Helge, Martin Luther Univ Halle Wittenberg, Bot Garden, Kirchtor 1, D-06108 Halle, Germany.
   Schuldt, Andreas, Georg August Univ Gottingen, Fac Forest Sci, Forest Nat Conservat, Busgenweg 3, D-37077 Gottingen, Germany.
   Ebeling, Anne, Friedrich Schiller Univ Jena, Inst Ecol \& Evolut, Dornburger Str 159, D-07743 Jena, Germany.
   Kunz, Matthias; von Oheimb, Goddert, Tech Univ Dresden, Inst Gen Ecol \& Environm Protect, PF 1117, D-01735 Tharandt, Germany.
   Staab, Michael; Fornoff, Felix; Klein, Alexandra-Maria, Univ Freiburg, Nat Conservat \& Landscape Ecol, Tennenbacher Str 4, D-79106 Freiburg, Germany.
   Staab, Michael, Univ Freiburg, Freiburg Inst Adv Studies FRIAS, Albertstr 19, D-79104 Freiburg, Germany.
   Guimaraes-Steinicke, Claudia; Weigelt, Alexandra; Wirth, Christian, Univ Leipzig, Systemat Bot \& Funct Biodivers, Johannisallee 21-23, D-04103 Leipzig, Germany.
   Bachmann, Doerte; Buchmann, Nina, Swiss Fed Inst Technol, Inst Agr Sci, Univ Str 2, CH-8092 Zurich, Switzerland.
   Durka, Walter, UFZ Helmholtz Ctr Environm Res, Dept Community Ecol, Theodor Lieser Str 4, D-06120 Halle, Germany.
   Fichtner, Andreas; Haerdtle, Werner, Leuphana Univ Luneburg, Inst Ecol, Univ Allee 1, D-21335 Luneburg, Germany.
   Hertzog, Lionel R., Univ Ghent, Terr Ecol Unit, KL Ledeganckstr 35, B-9000 Ghent, Belgium.
   Roscher, Christiane, UFZ, Physiol Divers, Helmholtz Ctr Environm Res, Permoserstr 15, D-04318 Leipzig, Germany.
   Schaller, Joerg, Univ Bayreuth, Bayreuth Ctr Ecol \& Environm Res BayCEER, Environm Geochem, Univ Str 30, D-95447 Bayreuth, Germany.
   Weisser, Wolfgang, Tech Univ Munich, Dept Ecol \& Ecosyst Management, Terr Ecol Res Grp, Hans Carl von Carlowitz Pl 2, D-85354 Freising Weihenstephan, Germany.
   Zhang, Jiayong, Zhejiang Normal Univ, Key Lab Wildlife Biotechnol Conservat \& Utilizat, Jinhua 321004, Zhejiang, Peoples R China.
   Eisenhauer, Nico, Univ Leipzig, Inst Biol, Deutsch Pl 5e, D-04103 Leipzig, Germany.},
DOI = {10.1038/s41467-019-09448-8},
Article-Number = {1460},
EISSN = {2041-1723},
Keywords-Plus = {SPECIES-DIVERSITY; FOOD WEBS; BIODIVERSITY; FOREST; HOMOGENIZATION;
   PATTERNS; BIOMASS; TRAITS},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {andreas.schuldt@forst.uni-goettingen.de},
Affiliations = {Martin Luther University Halle Wittenberg; Martin Luther University
   Halle Wittenberg; University of Gottingen; Friedrich Schiller University
   of Jena; Technische Universitat Dresden; University of Freiburg;
   University of Freiburg; Leipzig University; Swiss Federal Institutes of
   Technology Domain; ETH Zurich; Helmholtz Association; Helmholtz Center
   for Environmental Research (UFZ); Leuphana University Luneburg; Ghent
   University; Helmholtz Association; Helmholtz Center for Environmental
   Research (UFZ); University of Bayreuth; Technical University of Munich;
   Zhejiang Normal University; Leipzig University},
ResearcherID-Numbers = {Buchmann, Nina/E-6095-2011
   von Oheimb, Goddert/O-9483-2015
   Schaller, Jörg/E-2092-2013
   Eisenhauer, Nico/I-3191-2019
   Durka, Walter/E-4667-2010
   Weisser, Wolfgang W/B-9718-2014
   Fichtner, Andreas/AAP-3188-2021
   Weigelt, Alexandra/JCN-8278-2023
   Bruelheide, Helge/G-3907-2013
   Klein, Alexandra/J-5871-2016
   Haerdtle, Werner/B-2568-2016
   Wirth, Christian/A-4446-2016
   Fornoff, Felix/AAA-3776-2019
   Schuldt, Andreas/J-9429-2013
   Staab, Michael/I-6544-2019
   Guimaraes-Steinicke, Claudia/ABB-6472-2020
   Eisenhauer, Nico/I-5932-2012
   Kunz, Matthias/G-6711-2017
   },
ORCID-Numbers = {Buchmann, Nina/0000-0003-0826-2980
   von Oheimb, Goddert/0000-0001-7408-425X
   Schaller, Jörg/0000-0003-1996-0127
   Eisenhauer, Nico/0000-0002-0371-6720
   Durka, Walter/0000-0002-6611-2246
   Weisser, Wolfgang W/0000-0002-2757-8959
   Fichtner, Andreas/0000-0003-0499-4893
   Weigelt, Alexandra/0000-0001-6242-603X
   Bruelheide, Helge/0000-0003-3135-0356
   Klein, Alexandra/0000-0003-2139-8575
   Fornoff, Felix/0000-0003-0446-7153
   Schuldt, Andreas/0000-0002-8761-0025
   Staab, Michael/0000-0003-0894-7576
   Eisenhauer, Nico/0000-0002-0371-6720
   Kunz, Matthias/0000-0002-0541-3424
   Hertzog, Lionel/0000-0003-0869-9672
   Hardtle, Werner/0000-0002-5599-5792
   Guimaraes-Steinicke, Claudia Regina/0000-0001-7829-641X},
Funding-Acknowledgement = {German Research Foundation {[}DFG FOR 891/1-3, DFG FOR 1451];
   Sino-German Centre for Research Promotion {[}GZ 524, 592, 698, 699, 785,
   1020]; National Natural Science Foundation of China {[}NSFC 30710103907,
   30930005]; Friedrich Schiller University Jena; Max Planck Society; Swiss
   National Science Foundation (SNF); German Centre for Integrative
   Biodiversity Research (iDiv) Halle-Jena-Leipzig {[}DFG FZT 118];
   European Research Council (ERC) {[}677232]; Open Access Publication Fund
   of the Martin-Luther-University Halle-Wittenberg},
Funding-Text = {We thank Xuefei Yang, Chen Lin, Sabine Both, Xiaojuan Liu, Yang Bo,
   Keping Ma and all members of the BEF-China consortium who coordinated
   and helped with the establishment and maintenance of the experiment. We
   thank the technical staff of the Jena Experiment consortium for their
   work in maintaining the field site and many student helpers for weeding
   of the experimental plots and support during measurements. We
   acknowledge Eric Anton, Theo Blick, Frank Creutzburg, Gunter Kohler,
   Gerlinde Kratzsch, Michael Meyer, Christoph Muster, and Oliver Wiche for
   their tremendous work of grassland arthropod identification. We are
   grateful to Stefan Michalski for providing phylogenetic plant data. We
   are indebted to our many helpers who contributed to the sampling of
   arthropods and plant data in the experiments. We gratefully acknowledge
   funding by the German Research Foundation (DFG FOR 891/1-3), the
   Sino-German Centre for Research Promotion (GZ 524, 592, 698, 699, 785,
   and 1020), and the National Natural Science Foundation of China (NSFC
   30710103907 and 30930005). The Jena Experiment is funded by the German
   Research Foundation (DFG FOR 1451) with additional support from the
   Friedrich Schiller University Jena, the Max Planck Society, and the
   Swiss National Science Foundation (SNF). A. S., H. B., and N. E.
   acknowledge support by the German Centre for Integrative Biodiversity
   Research (iDiv) Halle-Jena-Leipzig (DFG FZT 118). N. E. acknowledges
   funding by the European Research Council (ERC Starting Grant; grant
   agreement no. 677232). We acknowledge the financial support of the Open
   Access PublicationFund of the Martin-Luther-University Halle-Wittenberg.
   We thank theBiodiversity Informatics Unit of iDiv for providingsupport
   with the data quality checks and uploading to the data repository.},
Number-of-Cited-References = {74},
Times-Cited = {119},
Usage-Count-Last-180-days = {12},
Usage-Count-Since-2013 = {122},
Journal-ISO = {Nat. Commun.},
Doc-Delivery-Number = {HQ9BX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000462722700007},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000718205500004,
Author = {Turner, Jennifer R. and Stanley, Jennifer Tehan},
Title = {Holding on to Pieces of the Past: Daily Reports of Nostalgia in a
   Life-Span Sample},
Journal = {EMOTION},
Year = {2021},
Volume = {21},
Number = {5},
Pages = {951-961},
Month = {AUG},
Abstract = {Nostalgia, the fond remembrance of one's past, is a common experience
   hypothesized to increase across the life span. Yet data on the specific
   features of nostalgia, such as daily frequency and associated affect,
   are scarce. This study sought to address this limitation by assessing
   the daily experience of nostalgia using experience-sampling methods. A
   life-span sample of 108 participants (47 young, 31 middle-aged, and 30
   older adults) completed a 2-week, twice-daily experience-sampling study
   that yielded data describing the frequency and emotions of everyday
   nostalgia. Multilevel logistic regression analyses supported increased
   nostalgia frequency at every life stage: Young adults were 60\% less
   likely to report nostalgia compared with middle-aged adults (odds ratio
   {[}OR] = .40), whereas older adults were 3 times more likely than
   middle-aged adults to report nostalgia (OR = 3.05). Additionally, the
   experience of nostalgia was associated with significant heterogeneity in
   positive and negative affect. Approximately 72\% of participants
   experienced an increase in positive affect, and 51\% experienced an
   increase in negative affect. For young and middle-aged adults, a change
   in positive affect was associated with a 2-times-larger increase in
   nostalgia likelihood, whereas a change in negative affect was more
   strongly associated with a nostalgia experience in older adults. The
   current study provides increased evidence for the affectively mixed
   nature of nostalgia and how the affective pattern differs for adults of
   different ages. Greater nostalgia frequency may be instrumental during
   life review when individuals make meaning of their lives, fulfilling
   developmental goals of late adulthood.},
Publisher = {AMER PSYCHOLOGICAL ASSOC},
Address = {750 FIRST ST NE, WASHINGTON, DC 20002-4242 USA},
Type = {Article},
Language = {English},
Affiliation = {Turner, JR (Corresponding Author), Penn State Univ, Coll Hlth \& Human Dev, Edna Bennett Pierce Prevent Res Ctr, 314 Biobehav Hlth Bldg, University Pk, PA 16802 USA.
   Turner, Jennifer R.; Stanley, Jennifer Tehan, Univ Akron, Dept Psychol, Akron, OH 44325 USA.},
DOI = {10.1037/emo0000980},
ISSN = {1528-3542},
EISSN = {1931-1516},
Keywords = {life-span development; daily assessment; naturalistic observation},
Keywords-Plus = {MINI-MENTAL-STATE; EMOTIONAL EXPERIENCE; SOCIAL CONNECTEDNESS;
   STATISTICAL POWER; TIME PERSPECTIVE; REMINISCENCE; MEMORY; CONCEPTIONS;
   IMPROVES},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Experimental},
Author-Email = {jrt5643@psu.edu},
Affiliations = {University System of Ohio; University of Akron},
ResearcherID-Numbers = {Stanley, Jennifer Tehan/J-2782-2019
   Turner, Jennifer Renee/ABA-3863-2020},
ORCID-Numbers = {Stanley, Jennifer Tehan/0000-0003-2297-9750
   Turner, Jennifer Renee/0000-0003-1105-9094},
Funding-Acknowledgement = {American Psychological Association Dissertation Research Grant; Dr. Paul
   E. Panek Endowed Scholarship in Psychology},
Funding-Text = {This work was supported by an American Psychological Association
   Dissertation Research Grant and the Dr. Paul E. Panek Endowed
   Scholarship in Psychology awarded to Jennifer R. Turner. We thank Maggie
   Allphin, Kenzie Delposen, and Lauren Knight for their assistance with
   data collection; Jacqueline Mogle, for her assistance in data analysis
   and interpretation; and the participants for their generous donation of
   time. This study was not preregistered. However, to further open science
   and replicability, all data and materials pertaining to this study will
   be made available to researchers via the Open Science Framework (OSF)
   Data Repository upon request.},
Number-of-Cited-References = {55},
Times-Cited = {20},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {21},
Journal-ISO = {Emotion},
Doc-Delivery-Number = {WW9CO},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000718205500004},
DA = {2024-01-15},
}

@article{ WOS:000563082800014,
Author = {Carpenter, Stephanie M. and Niedenthal, Paula M.},
Title = {Disrupting Facial Action Increases Risk Taking},
Journal = {EMOTION},
Year = {2020},
Volume = {20},
Number = {6},
Pages = {1084-1092},
Month = {SEP},
Abstract = {Sometimes risk involves taking actions that in and of themselves elicit
   emotion, often fearful emotions. Across two studies we test the
   hypothesis that preventing facial actions associated with fear and
   anxiety responses during a risky decision task leads to greater risk
   taking. We first demonstrate that while performing the balloon analogue
   risk task (Lejuez et al.. 2002), individuals make grimaces associated
   with anxious anticipation. In Study 1 (n = 120), experimental condition
   participants had inflexible medical tape attached to their foreheads to
   disrupt movement of the brow, and they wore a mouth guard that
   interfered with actions involving the mouth. Tape was also applied to
   control participants' faces, but it did not disrupt facial action, and
   they did not wear a mouth guard. All participants performed the balloon
   analogue risk task, in which a greater number of balloon pumps signals
   more risk taking. Study 2 (n = 202) served as a replication and minor
   extension that added a second risk task also predicted to elicit anxious
   anticipation (i.e., a jack-in-the-box toy). As hypothesized, disrupting
   the activation of facial muscles led to more balloon pumps and lever
   turns. Our findings suggest that facial expressions modulate risk
   taking.},
Publisher = {AMER PSYCHOLOGICAL ASSOC},
Address = {750 FIRST ST NE, WASHINGTON, DC 20002-4242 USA},
Type = {Article},
Language = {English},
Affiliation = {Carpenter, SM (Corresponding Author), Univ Wisconsin, Dept Psychol, 1202 West Johnson St, Madison, WI 53706 USA.
   Carpenter, Stephanie M.; Niedenthal, Paula M., Univ Wisconsin, Dept Psychol, 1202 West Johnson St, Madison, WI 53706 USA.},
DOI = {10.1037/emo0000597},
ISSN = {1528-3542},
EISSN = {1931-1516},
Keywords = {emotion; facial expression; risk; decision-making},
Keywords-Plus = {SOMATIC MARKER HYPOTHESIS; TASK BART; SENSATION SEEKING; EMOTION;
   PERCEPTION; FEEDBACK; EXPRESSION; MIMICRY; SMILE},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Experimental},
Author-Email = {smcarpen@umich.edu},
Affiliations = {University of Wisconsin System; University of Wisconsin Madison},
ResearcherID-Numbers = {Carpentetr, Stephanie/JDC-8173-2023},
Funding-Acknowledgement = {National Institute of Mental Health of the National Institutes of Health
   {[}T32MH018931]},
Funding-Text = {This publication was supported by the National Institute of Mental
   Health of the National Institutes of Health under Award T32MH018931.
   Data, materials, and the Study 2 preregistration can be found on the
   Open Science Framework (OSF) website
   (https://osf.io/njdq7/?view\_only\~{}6325 102f532445d18f02a2a239d268e7).
   Upon publication, the data files for the pretest and two studies
   reported here will be fully available on the OSF data repository website
   (https://osf.io/njdq7/files).},
Number-of-Cited-References = {46},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {17},
Journal-ISO = {Emotion},
Doc-Delivery-Number = {NF1ST},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000563082800014},
OA = {Green Accepted, Bronze},
DA = {2024-01-15},
}

@article{ WOS:000440124800003,
Author = {Dewe, Hayley and Watson, Derrick G. and Kessler, Klaus and Braithwaite,
   Jason J.},
Title = {The depersonalized brain: New evidence supporting a distinction between
   depersonalization and derealization from discrete patterns of autonomic
   suppression observed in a non-clinical sample},
Journal = {CONSCIOUSNESS AND COGNITION},
Year = {2018},
Volume = {63},
Pages = {29-46},
Month = {AUG},
Abstract = {Depersonalization and Derealization are characterised by feelings of
   detachment from one's bodily self/surroundings and a general emotional
   numbness. We explored predisposition to trait- based experiences of
   depersonalization/derealization-type experiences and autonomic arousal
   toward simulated body-threats, which were delivered to the participant's
   own body (i.e. Self) and when observed being delivered to another
   individual (i.e. Other). Ninety participants took part in an ``Implied
   Body-Threat Illusion{''} task (Dewe, Watson, \& Braithwaite, 2016) and
   autonomic arousal was recorded via standardised skin conductance
   responses and finger temperature. Autonomic suppression in response to
   threats delivered to the Self correlated with increases in trait-based
   depersonalization-type experiences. In contrast, autonomic suppression
   for threats delivered to Others correlated with trait-based
   derealization-like experiences. Body-temperature and anticipatory
   arousal did not correlate reliably with predisposition to
   depersonalization- or derealization-type experiences. The theoretical
   implications of these findings are discussed in terms of a fronto-limbic
   autonomic suppression mechanism.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Dewe, H (Corresponding Author), Univ Birmingham, Behav Brain Sci Ctr, Sch Psychol, Birmingham, W Midlands, England.
   Dewe, Hayley, Univ Birmingham, Behav Brain Sci Ctr, Sch Psychol, Birmingham, W Midlands, England.
   Watson, Derrick G., Univ Warwick, Dept Psychol, Coventry, W Midlands, England.
   Kessler, Klaus, Aston Univ, Aston Brain Ctr, Birmingham, W Midlands, England.
   Braithwaite, Jason J., Univ Lancaster, Dept Psychol, Lancaster, England.},
DOI = {10.1016/j.concog.2018.06.008},
ISSN = {1053-8100},
EISSN = {1090-2376},
Keywords = {Anomalous body experience; Depersonalization; Derealization;
   Dissociation; Multisensory integration; Self-consciousness; Skin
   conductance responses (SCRs)},
Keywords-Plus = {OF-BODY EXPERIENCE; RUBBER-HAND; FACIAL EXPRESSIONS; PERSPECTIVE-TAKING;
   NEURAL MECHANISMS; CAMBRIDGE DEPERSONALIZATION; MULTISENSORY
   INTEGRATION; PHYSIOLOGICAL CONDITION; SKIN-CONDUCTANCE; SELF-EXPERIENCE},
Research-Areas = {Psychology},
Web-of-Science-Categories  = {Psychology, Experimental},
Author-Email = {h.dewe944@gmail.com},
Affiliations = {University of Birmingham; University of Warwick; Aston University;
   Lancaster University},
ORCID-Numbers = {Braithwaite, Jason/0000-0003-1263-9410
   Dewe, Hayley/0000-0003-1757-0432
   Kessler, Klaus/0000-0001-7307-9539},
Funding-Acknowledgement = {Bial Foundation {[}51/14]; Bial Foundation; ESRC {[}ES/I019545/1]
   Funding Source: UKRI},
Funding-Text = {The current study complied with ethical guidance (ERN\_15-0384). This
   research was funded through a Bursary grant from the Bial Foundation
   (\#51/14) awarded to the last author (JJB). We sincerely thank the Bial
   Foundation for generously supporting our research, and thank all of our
   participants for taking part. In line with open-science protocols, the
   data for this study is available at the Lancaster University data
   repository (http://doLorg/10.17635/laricaster/researchdata/226).},
Number-of-Cited-References = {127},
Times-Cited = {21},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {18},
Journal-ISO = {Conscious. Cogn.},
Doc-Delivery-Number = {GO6DR},
Web-of-Science-Index = {Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000440124800003},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000463987100007,
Author = {Shiva, Javad Shafiei and Chandler, David G. and Kunkel, Kenneth E.},
Title = {Localized Changes in Heat Wave Properties Across the United States},
Journal = {EARTHS FUTURE},
Year = {2019},
Volume = {7},
Number = {3},
Pages = {300-319},
Month = {MAR},
Abstract = {Heat waves are an important type of extreme climate event and directly
   result in more than 130 deaths per year across the United States. Heat
   waves have been described by several attributes and combinations which
   constitute various event typologies. Attributes of heat waves from 10
   cities are analyzed over the period 1950-2016 to understand how these
   attributes determine variability in local heat waves and how climate
   change affects heat waves across the United States. This study uses
   eight definitions to differentiate heat waves and tests for temporal
   trends in key properties of heat waves over the period 1950-2016. At
   least five harmful attributes of heat waves have increased
   simultaneously for Dallas, Miami, New York, Phoenix, and Portland.Miami
   showed the greatest change in heat wave season length, frequency, and
   timing over the study period. Surprisingly, the greatest mean heat wave
   intensities above daily thresholds were for Bismarck, ND (+8.2 degrees
   C) and Syracuse, NY (+6.5 degrees C). Similar results across Baltimore,
   MD, Colorado Springs, CO, Dallas, TX, Des Moines, IA, Miami, FL, New
   York, NY, Phoenix, AZ, and Portland, OR, are presented to clarify the
   many quantitative differences in heat wave attributes and variance in
   quantification approaches across climates. This work explores the nexus
   of quantitative description and social construction of heat waves
   through the lens of the various regional metrics to describe heat waves.
   Ultimately, this assessment will guide the development of various
   strategies to help communities understand and prepare for heat
   resilience based on local heat wave components.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Shiva, JS (Corresponding Author), Syracuse Univ, Dept Civil \& Environm Engn, Syracuse, NY 13244 USA.
   Shiva, Javad Shafiei; Chandler, David G., Syracuse Univ, Dept Civil \& Environm Engn, Syracuse, NY 13244 USA.
   Kunkel, Kenneth E., North Carolina State Univ, North Carolina Inst Climate \& Satellites, Asheville, NC USA.},
DOI = {10.1029/2018EF001085},
EISSN = {2328-4277},
Keywords = {heat wave; climate change; Urban Heat Island; extreme climate events;
   heat wave properties and components; heat wave profile},
Keywords-Plus = {EXTREME WEATHER; COLD WAVES; CLIMATE-CHANGE; HOT SPELLS; URBAN FORM;
   MORTALITY; IMPACT; TEMPERATURE; EVENTS; RISK},
Research-Areas = {Environmental Sciences \& Ecology; Geology; Meteorology \& Atmospheric
   Sciences},
Web-of-Science-Categories  = {Environmental Sciences; Geosciences, Multidisciplinary; Meteorology \&
   Atmospheric Sciences},
Author-Email = {jshafiei@syr.edu},
Affiliations = {Syracuse University; North Carolina State University},
ResearcherID-Numbers = {Kunkel, Kenneth E/C-7280-2015
   Chandler, David/E-4543-2013},
ORCID-Numbers = {Kunkel, Kenneth E/0000-0001-6667-7047
   Chandler, David/0000-0002-8662-2892},
Funding-Acknowledgement = {Urban Resilience to Extremes Sustainability Research Network under
   National Science Foundation {[}AGS-1444755]},
Funding-Text = {Supporting data including annual heat wave components in each city based
   on both HW1 and HW2 definitions and a summary table of different heat
   wave definitions can be found with the online version of this article. R
   codes developed for heat wave components analysis are available in an
   online and open access data repository (Shafiei Shiva, 2018a, 2018b).
   The authors would like to thank two anonymous reviewers and the Editor
   Dr. Michael Ellis, for their comprehensive review, constructive
   comments, and suggestions that improved the clarity of the paper.
   Financial support for this work was provided via the Urban Resilience to
   Extremes Sustainability Research Network under National Science
   Foundation grant AGS-1444755.},
Number-of-Cited-References = {106},
Times-Cited = {52},
Usage-Count-Last-180-days = {22},
Usage-Count-Since-2013 = {103},
Journal-ISO = {Earth Future},
Doc-Delivery-Number = {HS6MX},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000463987100007},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000644275500006,
Author = {Xiang, Rong and Ma, Leyao and Yang, Mingyu and Zheng, Zetian and Chen,
   Xiaofang and Jia, Fujian and Xie, Fanfan and Zhou, Yiming and Li,
   Fuqiang and Wu, Kui and Zhu, Yafeng},
Title = {Increased expression of peptides from non-coding genes in cancer
   proteomics datasets suggests potential tumor neoantigens},
Journal = {COMMUNICATIONS BIOLOGY},
Year = {2021},
Volume = {4},
Number = {1},
Month = {APR 22},
Abstract = {Neoantigen-based immunotherapy has yielded promising results in clinical
   trials. However, it is limited to tumor-specific mutations, and is often
   tailored to individual patients. Identifying suitable tumor-specific
   antigens is still a major challenge. Previous proteogenomics studies
   have identified peptides encoded by predicted non-coding sequences in
   human genome. To investigate whether tumors express specific peptides
   encoded by non-coding genes, we analyzed published proteomics data from
   five cancer types including 933 tumor samples and 275 matched normal
   samples and compared these to data from 31 different healthy human
   tissues. Our results reveal that many predicted non-coding genes such as
   DGCR9 and RHOXF1P3 encode peptides that are overexpressed in tumors
   compared to normal controls. Furthermore, from the non-coding
   genes-encoded peptides specifically detected in cancers, we predict a
   large number of ``dark antigens{''} (neoantigens from non-coding genomic
   regions), which may provide an alternative source of neoantigens beyond
   standard tumor specific mutations. Rong Xiang et al. analyze the
   expression of non-coding genes encoded peptides in publicly-available
   proteomics data from five cancer types and matched controls. They
   identify peptides from non-coding genes including DGCR9 and RHOXF1P3
   that are upregulated in tumors compared to controls, suggesting that
   non-coding gene-encoded peptides may be a source of neoantigens in some
   cancers.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Zhu, YF (Corresponding Author), Sun Yat Sen Univ, Sun Yat Sen Mem Hosp, Med Res Ctr, Guangdong Prov Key Lab Malignant Tumor Epigenet \&, Guangzhou, Peoples R China.
   Xiang, Rong, Univ Chinese Acad Sci, BGI Educ Ctr, Shenzhen, Peoples R China.
   Xiang, Rong; Ma, Leyao; Yang, Mingyu; Zheng, Zetian; Chen, Xiaofang; Jia, Fujian; Xie, Fanfan; Li, Fuqiang; Wu, Kui, BGI Shenzhen, Shenzhen, Peoples R China.
   Ma, Leyao; Zhou, Yiming, Southeast Univ, Nanjing, Peoples R China.
   Zhu, Yafeng, Sun Yat Sen Univ, Sun Yat Sen Mem Hosp, Med Res Ctr, Guangdong Prov Key Lab Malignant Tumor Epigenet \&, Guangzhou, Peoples R China.
   Li, Fuqiang; Wu, Kui, BGI Shenzhen, Guangdong Prov Key Lab Human Dis Genom, Shenzhen Key Lab Genom, Shenzhen, Peoples R China.},
DOI = {10.1038/s42003-021-02007-2},
Article-Number = {496},
EISSN = {2399-3642},
Keywords-Plus = {PROTEOGENOMIC CHARACTERIZATION; REVEALS; PSEUDOGENES; TRANSLATION;
   DRAFT; CELLS; RNAS},
Research-Areas = {Life Sciences \& Biomedicine - Other Topics; Science \& Technology -
   Other Topics},
Web-of-Science-Categories  = {Biology; Multidisciplinary Sciences},
Author-Email = {zhuyaf@mail.sysu.edu.cn},
Affiliations = {Chinese Academy of Sciences; University of Chinese Academy of Sciences,
   CAS; Beijing Genomics Institute (BGI); Southeast University - China; Sun
   Yat Sen University; Beijing Genomics Institute (BGI)},
ResearcherID-Numbers = {Wu, Kui/JHT-4169-2023
   },
ORCID-Numbers = {Wu, Kui/0000-0002-6857-7231
   Zhou, Yiming/0000-0002-2109-4320},
Funding-Acknowledgement = {National Key Research and Development Program of China
   {[}2017YFC1311000]; GuangDong Science and Technology Department
   {[}2017B030314026]; Science, Technology and Innovation Commission of
   Shenzhen Municipality {[}JCYJ20160531193931852]; Science and Technology
   Key Project of Guangdong Province, China {[}2019B020229002]; Guangdong
   Enterprise Key Laboratory of Human Disease Genomics {[}2020B1212070028]},
Funding-Text = {This work was supported by grants from the National Key Research and
   Development Program of China (No. 2017YFC1311000); GuangDong Science and
   Technology Department (No. 2017B030314026); Science, Technology and
   Innovation Commission of Shenzhen Municipality (No.
   JCYJ20160531193931852); Science and Technology Key Project of Guangdong
   Province, China (No. 2019B020229002); Guangdong Enterprise Key
   Laboratory of Human Disease Genomics (2020B1212070028). We are thankful
   that the Clinical Proteomic Tumor Analysis Consortium (NCI/NIH) for
   sharing the data and ProteomeXchange Consortium for providing an open
   access proteomics data repository. We would like to thank China National
   GeneBank (https://db.cngb.org), Shenzhen, China for providing computing
   resources that support the data analysis for the paper.},
Number-of-Cited-References = {54},
Times-Cited = {17},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {16},
Journal-ISO = {Commun. Biol.},
Doc-Delivery-Number = {RT2DU},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000644275500006},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000776466100005,
Author = {Havermann, Felix and Ghirardo, Andrea and Schnitzler, Joerg-Peter and
   Nendel, Claas and Hoffmann, Mathias and Kraus, David and Grote, Ruediger},
Title = {Modeling Intra- and Interannual Variability of BVOC Emissions From
   Maize, Oil-Seed Rape, and Ryegrass},
Journal = {JOURNAL OF ADVANCES IN MODELING EARTH SYSTEMS},
Year = {2022},
Volume = {14},
Number = {3},
Month = {MAR},
Abstract = {Air chemistry is affected by the emission of biogenic volatile organic
   compounds (BVOCs), which originate from almost all plants in varying
   qualities and quantities. They also vary widely among different crops,
   an aspect that has been largely neglected in emission inventories. In
   particular, bioenergy-related species can emit mixtures of highly
   reactive compounds that have received little attention so far. For such
   species, long-term field observations of BVOC exchange from relevant
   crops covering different phenological phases are scarcely available.
   Therefore, we measured and modeled the emission of three prominent
   European bioenergy crops (maize, ryegrass, and oil-seed rape) for full
   rotations in north-eastern Germany. Using a proton transfer
   reaction-mass spectrometer combined with automatically moving large
   canopy chambers, we were able to quantify the characteristic seasonal
   BVOC flux dynamics of each crop species. The measured BVOC fluxes were
   used to parameterize and evaluate the BVOC emission module (JJv) of the
   physiology-oriented LandscapeDNDC model, which was enhanced to cover de
   novo emissions as well as those from plant storage pools. Parameters are
   defined for each compound individually. The model is used for simulating
   total compound-specific reactivity over several years and also to
   evaluate the importance of these emissions for air chemistry. We can
   demonstrate substantial differences between the investigated crops with
   oil-seed rape having 37-fold higher total annual emissions than maize.
   However, due to a higher chemical reactivity of the emitted blend in
   maize, potential impacts on atmospheric OH-chemistry are only 6-fold
   higher.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Grote, R (Corresponding Author), Karlsruhe Inst Technol, Inst Meterol \& Climate Res Atmospher Environm Res, Garmisch Partenkirchen, Germany.
   Havermann, Felix; Kraus, David; Grote, Ruediger, Karlsruhe Inst Technol, Inst Meterol \& Climate Res Atmospher Environm Res, Garmisch Partenkirchen, Germany.
   Havermann, Felix, Ludwig Maximilians Univ Munchen, Dept Geog, Munich, Germany.
   Nendel, Claas; Hoffmann, Mathias, Leibniz Ctr Agr Landscape Res ZALF, Muncheberg, Germany.
   Ghirardo, Andrea; Schnitzler, Joerg-Peter, Helmholtz Zentrum Munchen, Res Unit Environm Simulat EUS, Inst Biochem Plant, Neuherberg, Germany.
   Nendel, Claas, Univ Potsdam, Inst Biochem \& Biol, Potsdam, Germany.
   Nendel, Claas, Czech Acad Sci, Global Change Res Inst, Brno, Czech Republic.},
DOI = {10.1029/2021MS002683},
Article-Number = {e2021MS002683},
EISSN = {1942-2466},
Keywords = {biogenic volatile organic compounds; process-based modeling; Zea mays;
   Brassica napus; Lolium multiflorum; plant ontogenetic stage},
Keywords-Plus = {VOLATILE ORGANIC-COMPOUNDS; BIOGENIC VOC EMISSIONS; ROTATION COPPICE
   WILLOW; AIR-QUALITY IMPACTS; COMPOUND EMISSIONS; TEMPERATURE RESPONSE;
   ISOPRENE EMISSIONS; BIOCHEMICAL-MODEL; MEGAN MODEL; PHOTOSYNTHESIS},
Research-Areas = {Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Meteorology \& Atmospheric Sciences},
Author-Email = {ruediger.grote@kit.edu},
Affiliations = {Helmholtz Association; Karlsruhe Institute of Technology; University of
   Munich; Leibniz Zentrum fur Agrarlandschaftsforschung (ZALF); Helmholtz
   Association; Helmholtz-Center Munich - German Research Center for
   Environmental Health; University of Potsdam; Czech Academy of Sciences;
   Global Change Research Centre of the Czech Academy of Sciences},
ResearcherID-Numbers = {Grote, Rüdiger/A-7350-2013
   Havermann, Felix/JPW-9067-2023
   Nendel, Claas/C-8844-2013
   Ghirardo, Andrea/P-1764-2019
   Schnitzler, Joerg-Peter/C-5268-2011
   Kraus, David/B-7663-2016},
ORCID-Numbers = {Grote, Rüdiger/0000-0001-6893-6890
   Nendel, Claas/0000-0001-7608-9097
   Havermann, Felix/0000-0001-8849-0195
   Ghirardo, Andrea/0000-0003-1973-4007
   Hoffmann, Mathias/0000-0002-2776-1403
   Schnitzler, Joerg-Peter/0000-0002-9825-867X
   Kraus, David/0000-0003-2485-8389},
Funding-Acknowledgement = {Federal Ministry of Food and Agriculture through the Agency for
   Renewable Resources (FNR) {[}FKZ 22006414, 12NR257]; Karlsruhe Institute
   of Technology; Helmholtz Research School ``Mechanisms and Interactions
   of Climate Change in Mountain Regions{''} (MICMoR) through KIT/IMK-IFU;
   Projekt DEAL},
Funding-Text = {This study is incorporated into the CarboZALF project providing the
   automatic chambers equipped with instruments for meteorological
   observations and gas exchange under the lead of Jurgen Augustin from
   ZALF. We are especially grateful to Gernot Verch, head of the ZALF
   research station in Dedelow and to Marten Schmidt for maintenance and
   setting up most of the measuring infrastructure. We also want to thank
   Steffen Klatt for his IT support with LandscapeDNDC, Christof Lorenz for
   his help with the data repository, as well as two anonymous reviewers
   for their valuable comments. The project has been financed by the
   Federal Ministry of Food and Agriculture (FKZ 22006414 and 12NR257)
   through the Agency for Renewable Resources (FNR). We also acknowledge
   support by the KIT-Publication Fund of the Karlsruhe Institute of
   Technology for publishing open-access and by a Fellowship in the
   Helmholtz Research School ``Mechanisms and Interactions of Climate
   Change in Mountain Regions{''} (MICMoR) through KIT/IMK-IFU. Open access
   funding enabled and organized by Projekt DEAL.},
Number-of-Cited-References = {104},
Times-Cited = {1},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {37},
Journal-ISO = {J. Adv. Model. Earth Syst.},
Doc-Delivery-Number = {0E1TB},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000776466100005},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000353908000001,
Author = {Fillmore, Paul T. and Phillips-Meek, Michelle C. and Richards, John E.},
Title = {Age-specific MRI brain and head templates for healthy adults from 20
   through 89 years of age},
Journal = {FRONTIERS IN AGING NEUROSCIENCE},
Year = {2015},
Volume = {7},
Month = {APR 8},
Abstract = {This study created and tested a database of adult, age-specific MRI
   brain and head templates. The participants included healthy adults from
   20 through 89 years of age. The templates were done in five-year,
   10-year, and multi-year intervals from 20 through 89 years, and consist
   of average T1W for the head and brain, and segmenting priors for gray
   matter (GM), white matter (WM), and cerebrospinal fluid (CSF). It was
   found that age-appropriate templates provided less biased tissue
   classification estimates than age-inappropriate reference data and
   reference data based on young adult templates. This database is
   available for use by other investigators and clinicians for their MRI
   studies, as well as other types of neuroimaging and electrophysiological
   research.(1)},
Publisher = {FRONTIERS MEDIA SA},
Address = {PO BOX 110, EPFL INNOVATION PARK, BUILDING I, LAUSANNE, 1015,
   SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Richards, JE (Corresponding Author), Univ S Carolina, Dept Psychol, 1800 Gervais St, Columbia, SC 29208 USA.
   Fillmore, Paul T., Univ S Carolina, Dept Commun Sci \& Disorders, Columbia, SC 29208 USA.
   Phillips-Meek, Michelle C.; Richards, John E., Univ S Carolina, Dept Psychol, Columbia, SC 29208 USA.
   Phillips-Meek, Michelle C., Limestone Coll, Dept Psychol, Gaffney, SC USA.
   Richards, John E., Univ S Carolina, Inst Mind \& Brain, Columbia, SC 29208 USA.},
DOI = {10.3389/fnagi.2015.00044},
Article-Number = {44},
ISSN = {1663-4365},
Keywords = {MRI; aging; adult; segmentation; templates},
Keywords-Plus = {VOXEL-BASED MORPHOMETRY; DEMENTED OLDER-ADULTS; OPEN ACCESS SERIES;
   IMAGE REGISTRATION; NIH MRI; SPATIAL NORMALIZATION; PROBABILISTIC ATLAS;
   GRAY-MATTER; SEGMENTATION; YOUNG},
Research-Areas = {Geriatrics \& Gerontology; Neurosciences \& Neurology},
Web-of-Science-Categories  = {Geriatrics \& Gerontology; Neurosciences},
Author-Email = {richards-john@sc.edu},
Affiliations = {University of South Carolina System; University of South Carolina
   Columbia; University of South Carolina System; University of South
   Carolina Columbia; University of South Carolina System; University of
   South Carolina Columbia},
ORCID-Numbers = {Richards, John E./0000-0002-8283-4468
   Fillmore, Paul/0000-0002-9997-2170},
Funding-Acknowledgement = {NIH {[}R37 HD18942]; National Institute of Child Health and Human
   Development; National Institute on Drug Abuse; National Institute of
   Mental Health; National Institute of Neurological Disorders and Stroke
   {[}N01-HD02-3343, N01-MH9-0002, N01-NS-9-2314, N01-NS-9-2315,
   N01-NS-9-2316, N01-NS-9-2317, N01-NS-9-2319, N01-NS-9-2320]; Biomedical
   Informatics Research Network (BIRN) {[}P50 AG05681, P01 AG03991, R01
   AG021910, P50 MH071616, U24 RR021382, R01 MH56584]},
Funding-Text = {This work was supported by the NIH grant to JER, \#R37 HD18942. We are
   grateful for Wanze Xie's assistance in creating Figure 8. Data used in
   the preparation of this article were obtained from the NTH Pediatric MRI
   Data Repository created by the NIHPD. This is a multisite, longitudinal
   study of typically developing children from ages newborn through young
   adulthood conducted by the Brain Development Cooperative Group and
   supported by the National Institute of Child Health and Human
   Development, the National Institute on Drug Abuse, the National
   Institute of Mental Health, and the National Institute of Neurological
   Disorders and Stroke (Contract \#s N01-HD02-3343, N01-MH9-0002, and
   N01-NS-9-2314, -2315, -2316, -2317, -2319 and -2320). A listing of the
   participating sites and a complete listing of the study investigators
   can be found at
   http://www.bic.mni.mcgill.ca/nihpd/info/participating\_centers.html.
   Data used in preparation of this article were also obtained from the
   OASIS, a project aimed at making MRI data sets of the brain freely
   available to the scientific community. OASIS is made available by the
   Washington University Alzheimer's Disease Research Center, Dr. Randy
   Buckner at the Howard Hughes Medical Institute (HHMI) at Harvard
   University, the Neuroinformatics Research Group (NRG) at Washington
   University School of Medicine, and the Biomedical Informatics Research
   Network (BIRN). Contract \#s: P50 AG05681, P01 AG03991, R01 AG021910,
   P50 MH071616, U24 RR021382, and R01 MH56584.},
Number-of-Cited-References = {65},
Times-Cited = {73},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Front. Aging Neurosci.},
Doc-Delivery-Number = {CH3DV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000353908000001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000446873700001,
Author = {Lii-Rosales, Ann and Han, Yong and Yu, Ka Man and Jing, Dapeng and
   Anderson, Nathaniel and Vaknin, David and Tringides, Michael C. and
   Evans, James W. and Altman, Michael S. and Thiel, Patricia A.},
Title = {Reverse-engineering of graphene on metal surfaces: a case study of
   embedded ruthenium},
Journal = {NANOTECHNOLOGY},
Year = {2018},
Volume = {29},
Number = {50},
Month = {DEC 14},
Abstract = {Using scanning tunneling microscopy, x-ray photoelectron spectroscopy,
   and x-ray absorption spectroscopy, we show that Ru forms metallic
   nanoislands on graphite, covered by a graphene monolayer. These islands
   are air-stable, contain 2-4 layers of Ru, and have diameters on the
   order of 10 nm. To produce these nanoislands two conditions must be met
   during synthesis. The graphite surface must be ion-bombarded, and
   subsequently held at an elevated temperature (1000-1180 K) during Ru
   deposition. A coincidence lattice forms between the graphene overlayer
   and the Ru island top. Its characteristics-coincidence lattice constant,
   corrugation amplitude, and variation of carbon lattice appearance within
   the unit cell-closely resemble the well-established characteristics of
   single-layer graphene on the (0001) surface of bulk Ru. Quantitative
   analysis of the graphene lattice in relation to the coincidence lattice
   on the island tops show that the two-dimensional lattice constant of the
   underlying metal equals that of bulk Ru(0001), within experimental
   error. The embedded Ru islands are energetically favored over on-top
   (adsorbed) islands, based on density-functional-theory calculations for
   Ru films with 1-3 Ru layers. We propose a formation mechanism in which
   Ru atoms intercalate via defects that act as entry portals to the carbon
   galleries, followed by nucleation and growth in the galleries. In this
   model, high deposition temperature is necessary to prevent blockage of
   entry portals.},
Publisher = {IOP PUBLISHING LTD},
Address = {TEMPLE CIRCUS, TEMPLE WAY, BRISTOL BS1 6BE, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Thiel, PA (Corresponding Author), Ames Lab, Ames, IA 50011 USA.
   Thiel, PA (Corresponding Author), Iowa State Univ, Dept Chem, Ames, IA 50011 USA.
   Thiel, PA (Corresponding Author), Iowa State Univ, Dept Mat Sci \& Engn, Ames, IA 50011 USA.
   Lii-Rosales, Ann; Han, Yong; Jing, Dapeng; Anderson, Nathaniel; Vaknin, David; Tringides, Michael C.; Evans, James W.; Thiel, Patricia A., Ames Lab, Ames, IA 50011 USA.
   Lii-Rosales, Ann; Thiel, Patricia A., Iowa State Univ, Dept Chem, Ames, IA 50011 USA.
   Yu, Ka Man; Altman, Michael S., Hong Kong Univ Sci \& Technol, Dept Phys, Hong Kong, Hong Kong, Peoples R China.
   Jing, Dapeng, Iowa State Univ, Mat Anal \& Res Lab, Ames, IA 50011 USA.
   Anderson, Nathaniel; Vaknin, David; Tringides, Michael C.; Evans, James W., Iowa State Univ, Dept Phys \& Astron, Ames, IA 50011 USA.
   Thiel, Patricia A., Iowa State Univ, Dept Mat Sci \& Engn, Ames, IA 50011 USA.},
DOI = {10.1088/1361-6528/aae1e3},
Article-Number = {505601},
ISSN = {0957-4484},
EISSN = {1361-6528},
Keywords = {graphite; ruthenium; intercalation; surface; STM; DFT; moire
   superlattice},
Keywords-Plus = {GRAPHITE SURFACES; INTERCALATION COMPOUNDS; ELECTRONIC-STRUCTURE;
   EPITAXIAL GRAPHENE; RU(0001); DEFECTS; RU; SPECTRA; VACANCY; GROWTH},
Research-Areas = {Science \& Technology - Other Topics; Materials Science; Physics},
Web-of-Science-Categories  = {Nanoscience \& Nanotechnology; Materials Science, Multidisciplinary;
   Physics, Applied},
Author-Email = {pthiel@ameslab.gov},
Affiliations = {United States Department of Energy (DOE); Ames National Laboratory; Iowa
   State University; Hong Kong University of Science \& Technology; Iowa
   State University; Iowa State University; Iowa State University},
ResearcherID-Numbers = {Vaknin, David/B-3302-2009
   Han, Yong/L-7966-2019
   Anderson, Nathaniel/AAH-1862-2020
   Yu, Ka Man/R-2648-2017
   Altman, Michael/JQV-5184-2023
   Jing, Dapeng/M-3455-2014
   },
ORCID-Numbers = {Vaknin, David/0000-0002-0899-9248
   Anderson, Nathaniel/0000-0002-3172-8403
   Yu, Ka Man/0000-0001-8240-5105
   Jing, Dapeng/0000-0001-7600-7071
   Thiel, Patricia/0000-0003-4195-0216
   Lii-Rosales, Ann/0000-0002-8218-248X},
Funding-Acknowledgement = {US Department of Energy (DOE), Office of Science, Basic Energy Sciences,
   Materials Sciences and Engineering Division; National Science Foundation
   {[}ACI-1548562]; US DOE {[}DE-AC02-06CH11357]; Hong Kong Research Grants
   Council {[}600113]; DOE, Office of Science, Basic Energy Sciences,
   Chemical Sciences, Geosciences, and Biosciences Division; 
   {[}DE-AC02-07CH11358];  {[}DE-AC02-05CH11231]},
Funding-Text = {This work was supported mainly by the US Department of Energy (DOE),
   Office of Science, Basic Energy Sciences, Materials Sciences and
   Engineering Division. Research was performed at the Ames Laboratory,
   which is operated by Iowa State University under contract No.
   DE-AC02-07CH11358. DFT calculations used resources of the National
   Energy Research Scientific Computing Center (NERSC), a US DOE Office of
   Science User Facility operated under contract No. DE-AC02-05CH11231, and
   also used the Extreme Science and Engineering Discovery Environment
   (XSEDE), which is supported by National Science Foundation grant No.
   ACI-1548562. Use of the Advanced Photon Source, an Office of Science
   User Facility operated for the US Department of Energy (DOE) Office of
   Science by Argonne National Laboratory, is supported by the US DOE under
   Contract No. DE-AC02-06CH11357. The experimental work was performed or
   supervised by ALR, DJ, NA, DV, MCT, and PAT. Theoretical work was
   performed or supervised by YH and JWE. KMY and MSA performed
   quantitative analyses on the lattice constants and orientations of
   embedded Ru islands. KMY and MSA gratefully acknowledge support from the
   Hong Kong Research Grants Council under grant 600113. JWE's
   participation in the theoretical work was supported by the DOE, Office
   of Science, Basic Energy Sciences, Chemical Sciences, Geosciences, and
   Biosciences Division. The data presented in this paper are available in
   DataShare (http://instr.iastate.libguides.com/datashare/home), an open
   data repository managed by Iowa State University.},
Number-of-Cited-References = {65},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {48},
Journal-ISO = {Nanotechnology},
Doc-Delivery-Number = {GW4HR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000446873700001},
OA = {Green Published},
DA = {2024-01-15},
}

@article{ WOS:000360381400021,
Author = {Sato, Natsuo and Kadokura, Akira and Tanaka, Yoshimasa and Nishiyama,
   Takanori and Hori, Tomoaki and Yukimatu, Akira Sessai},
Title = {Omega band pulsating auroras observed onboard THEMIS spacecraft and on
   the ground},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2015},
Volume = {120},
Number = {7},
Pages = {5524-5544},
Month = {JUL},
Abstract = {We examined a fortuitous case of an omega band pulsating aurora observed
   simultaneously on the ground at Sanikiluaq in Canada and onboard the
   Time History of Events and Macroscale Interactions during Substorm
   (THEMIS) spacecraft on 1 March 2011. We observed almost the entire
   process of the generation of the omega band aurora from the initial
   growth to the declining through expansion period. The omega band aurora
   grew from a faint seed, not via distortion of a preexisting east-west
   band aurora. The size scale of the omega band aurora during the maximum
   period was similar to 500km in the north-south direction and similar to
   200km in the east-west direction. The mesoscale omega band aurora
   consisted of more than 15 patches of complex-shaped small-scale auroras.
   Each patch contained an intense pulsating aurora with a recurrent period
   of similar to 9-12s and a poleward moving form. The footprints of the
   THEMIS D and THEMIS E spacecraft crossed the poleward part of the omega
   band aurora. THEMIS D observed significant signatures in the
   electromagnetic fields and particles associated with the time at which
   the spacecraft crossed the omega band aurora. In particular, it was
   found that the Y and Z components of the DC electric field intensity,
   especially the Z component, modulated with almost the same period as
   that of the optical pulsating auroras. The electrostatic low-frequency
   waves of less than 30Hz showed quasiperiodic intensity variations
   similar to those of the DC electric field. These observations suggest
   that DC electric field variation and low-frequency electrostatic waves
   may play important roles in the driving mechanism of omega band
   pulsating auroras.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Sato, N (Corresponding Author), Natl Inst Polar Res, Tokyo, Japan.
   Sato, Natsuo; Kadokura, Akira; Tanaka, Yoshimasa; Nishiyama, Takanori; Yukimatu, Akira Sessai, Natl Inst Polar Res, Tokyo, Japan.
   Sato, Natsuo; Kadokura, Akira; Tanaka, Yoshimasa; Nishiyama, Takanori; Yukimatu, Akira Sessai, SOKENDAI, Yokohama, Kanagawa, Japan.
   Hori, Tomoaki, Nagoya Univ, Solar Terr Environm Lab, Nagoya, Aichi 4648601, Japan.},
DOI = {10.1002/2015JA021382},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords = {pulsating aurora; omega band aurora; THEMIS; torch aurora; aurora patch;
   electric field},
Keywords-Plus = {CONJUGATE AREAS; FAST SATELLITE; MAGNETOMETER; ELECTRODYNAMICS;
   MAGNETOSPHERE; OBSERVATORIES; DISTURBANCES; FLUCTUATIONS; ELECTRONS;
   SUBSTORM},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {nsato@nipr.ac.jp},
Affiliations = {Research Organization of Information \& Systems (ROIS); National
   Institute of Polar Research (NIPR) - Japan; Nagoya University},
ResearcherID-Numbers = {Nishiyama, Takanori/D-5546-2016
   Nishiyama, Takanori/ABA-2671-2020
   },
ORCID-Numbers = {Nishiyama, Takanori/0000-0002-3648-6589
   Nishiyama, Takanori/0000-0002-3648-6589
   Hori, Tomoaki/0000-0001-8451-6941},
Funding-Acknowledgement = {Inter-university Upper atmosphere Global Observation NETwork (IUGONET)
   project - Ministry of Education, Culture, Sports, Science and Technology
   of Japan; NIPR publication subsidy; NASA {[}NAS5-02099]; CSA
   {[}9F007-046101];  {[}26247082];  {[}15H02628];  {[}25287128];
   Grants-in-Aid for Scientific Research {[}15H02628, 15K05305, 25287129,
   26247082] Funding Source: KAKEN},
Funding-Text = {This work was partially supported by a Grant-in-Aid for Scientific
   Research A (26247082, 15H02628), and B (25287128), and the
   Inter-university Upper atmosphere Global Observation NETwork (IUGONET)
   project funded by the Ministry of Education, Culture, Sports, Science
   and Technology of Japan. Part of the work of T.H. has been done at
   ERG-Science Center operated by ISAS/JAXA and STEL/Nagoya University. The
   production of this paper was supported by an NIPR publication subsidy.
   The authors acknowledge NASA contract NAS5-02099 for the use of data
   from the THEMIS mission. Specifically, we thank S. Mende and E. Donovan
   for the use of the ASI data; J. W. Bonnell and F. S. Mozer for the use
   of EFI data; C. W. Carlson and J. P. McFadden for the use of ESA data;
   K. H. Glassmeier, U. Auster, and W. Baumjohann for the use of FGM data;
   and O. Le Contel and A. Roux for the use of SCM data. Deployment and
   data retrieval of the THEMIS ASIs were partly supported by CSA contract
   9F007-046101. THEMIS probes, geomagnetic field, and all-sky image data
   are available through the open data repository at UC Berkeley at
   http://themis.ssl.berkeley.edu/index.shtml. The authors also thank World
   Data Center for Geomagnetism, Kyoto for providing the Dst index at
   http://wdc.kugi.kyoto-u.ac.jp/dstdir/index.html. OMNI solar wind data
   were provided through the Coordinated Data AnalysisWeb at
   http://cdaweb.gsfc.nasa.gov/istp\_public/.},
Number-of-Cited-References = {66},
Times-Cited = {9},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {CQ1TF},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000360381400021},
DA = {2024-01-15},
}

@article{ WOS:000564581100004,
Author = {Braithwaite, Jason J. and Watson, Derrick G. and Dewe, Hayley},
Title = {The <i>Body</i>-<i>Threat Assessment Battery</i> (<i>BTAB</i>): A new
   instrument for the quantification of threat-related autonomic affective
   responses induced via dynamic movie clips},
Journal = {INTERNATIONAL JOURNAL OF PSYCHOPHYSIOLOGY},
Year = {2020},
Volume = {155},
Pages = {16-31},
Month = {SEP},
Abstract = {We present a new instrument for the assessment of responses to
   threat-related imagery directed towards a human body - the Body-Threat
   Assessment Battery (BTAB). The BTAB consists of a series of
   high-definition dynamic clips depicting body-threats and matched
   non-threat baseline behaviours. For body-threat stimuli a perspective
   manipulation was included to assess the effects of viewing threats from
   the point-of-view of the observer (POV) or from an external/exocentric
   perspective (EXO). Green-screen technology was used so that extraneous
   background information could be removed and standardised in
   post-production. Categorical normative data for psychological ratings
   (valence, arousal and pain), psychophysiological, phasic skin
   conductance responses (SCRs) and tonic skin conductance levels (SCLs)
   were obtained for all stimuli. Body-threat stimuli evoked significantly
   higher psychological ratings of arousal and pain, with more negative
   ratings of valence, relative to baseline stimuli. In addition, threat
   stimuli also had an increased efficacy at evoking SCRs, and these were
   significantly stronger relative to baseline stimuli. There were no
   effects of perspective on psychophysiological or psychological responses
   to threat imagery. The findings are discussed in the context of the
   utility and scope of the BTAB for supporting neurocognitive
   investigations of aversive imagery and body-threats specifically in the
   study of embodiment, body-processing and self-consciousness.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29a, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Braithwaite, JJ (Corresponding Author), Univ Lancaster, Dept Psychol, Lancaster LA1 4YF, England.
   Braithwaite, Jason J., Univ Lancaster, Dept Psychol, Lancaster LA1 4YF, England.
   Watson, Derrick G., Univ Warwick, Dept Psychol, Coventry CV4 7AL, W Midlands, England.
   Dewe, Hayley, Univ Durham, Dept Psychol, Durham DH1 3LE, England.},
DOI = {10.1016/j.ijpsycho.2020.04.018},
ISSN = {0167-8760},
EISSN = {1872-7697},
Keywords = {Body threat imagery; Self-consciousness; Body image; Autonomic
   responses; Skin conductance responses; Psychophysiology},
Keywords-Plus = {SKIN-CONDUCTANCE RESPONSES; PICTURE SYSTEM IAPS; FACIAL EXPRESSIONS;
   MULTISENSORY INTEGRATION; INDIVIDUAL-DIFFERENCES; ANTERIOR CINGULATE;
   ANXIETY DISORDER; STARTLE REFLEX; HUMAN AMYGDALA; EMOTION},
Research-Areas = {Psychology; Neurosciences \& Neurology; Physiology},
Web-of-Science-Categories  = {Psychology, Biological; Neurosciences; Physiology; Psychology;
   Psychology, Experimental},
Author-Email = {j.j.braithwaite@lancaster.ac.uk},
Affiliations = {Lancaster University; University of Warwick; Durham University},
ORCID-Numbers = {Braithwaite, Jason/0000-0003-1263-9410
   Dewe, Hayley/0000-0003-1757-0432},
Funding-Acknowledgement = {Bial Foundation {[}51/14]},
Funding-Text = {This research was funded by a Bursary Grant from the Bial Foundation
   (\#51/14) awarded to the first author (JJB). We thank the foundation for
   their generous support of this work. This work complied with ethical
   practices and sought informed consent from all participants (ethics
   reference ERN\_15-0384 and FST 16039) in line with institutional
   practice. In line with open-science data practices, the data from this
   project are available at the Lancaster University Data repository
   (https://dx.doi.org/10.17635/lancaster/researchdata/362).},
Number-of-Cited-References = {118},
Times-Cited = {1},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Int. J. Psychophysiol.},
Doc-Delivery-Number = {NH3NT},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Social Science Citation Index (SSCI)},
Unique-ID = {WOS:000564581100004},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000775205500012,
Author = {Rokhuma, Samuel Lalthazuala and Changmai, Bishwajit and Kress, Thomas
   and Wheatley, Andrew E. H.},
Title = {A one-pot route to tunable sugar-derived sulfonated carbon catalysts for
   sustainable production of biodiesel by fatty acid esterification},
Journal = {RENEWABLE ENERGY},
Year = {2022},
Volume = {184},
Pages = {908-919},
Month = {JAN},
Abstract = {Carbon-based solid acid catalysts possessing up to 1.29 mmol g(-1)-SO3H
   active centers were synthesized from glucose via an efficient one-pot
   hydrothermal carbonization-sulfonation without the need for high
   temperatures. Catalysts combined aromatic structure with hydrophilic-OH
   and-COOH groups and a high density of -SO3H centers (up to a total acid
   density of 5.31 mmol g(-1)). The level of -SO3H (0.81-1.29 mmol g(-1))
   proved synthetically tunable. The relevance of the catalyst to the
   production of more sustainable fuels was tested using oleic acid (a free
   fatty acid whose esterification can be employed as a model for biodiesel
   production). Optimizing catalyst and conditions (20:1 MeOH:oleic acid
   molar ratio, 5 wt \% catalyst loading wrt oleic acid, 80 degrees C, 120
   min) enabled oleic acid esterification to the corresponding methyl
   oleate (a biodiesel component) with 97.5 +/- 0.4\% conversion and a low
   37.6 kJ mol(-1) activation energy. Activity loss upon re-use of the
   catalyst was proved to be by desulfonation and could be completely
   reversed. Hence, re-sulfonation of spent catalyst by a one-step process
   again delivered a 97.4 +/- 0.5\% conversion of oleic acid. (c) 2021
   Elsevier Ltd. All rights reserved.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Wheatley, AEH (Corresponding Author), Univ Cambridge, Yusuf Hamied Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England.
   Rokhuma, SL (Corresponding Author), Natl Inst Technol Silchar, Dept Chem, Silchar 788010, Assam, India.
   Rokhuma, Samuel Lalthazuala; Kress, Thomas; Wheatley, Andrew E. H., Univ Cambridge, Yusuf Hamied Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England.
   Rokhuma, Samuel Lalthazuala; Changmai, Bishwajit, Natl Inst Technol Silchar, Dept Chem, Silchar 788010, Assam, India.},
DOI = {10.1016/j.renene.2021.12.001},
ISSN = {0960-1481},
EISSN = {1879-0682},
Keywords = {Biodiesel; Carbonization; Esterification; Hydrothermal synthesis;
   Sulfonation; Activation energy},
Keywords-Plus = {WASTE COOKING OIL; LIQUID-PHASE OXIDATIONS; SOLID-ACID; OLEIC-ACID;
   HETEROGENEOUS CATALYSTS; AMORPHOUS-CARBON; TRANSESTERIFICATION;
   PERFORMANCE; HYDROLYSIS; CELLULOSE},
Research-Areas = {Science \& Technology - Other Topics; Energy \& Fuels},
Web-of-Science-Categories  = {Green \& Sustainable Science \& Technology; Energy \& Fuels},
Author-Email = {aehw2@cam.ac.uk
   aehw2@cam.ac.uk},
Affiliations = {University of Cambridge; National Institute of Technology (NIT System);
   National Institute of Technology Silchar},
ResearcherID-Numbers = {Changmai, Dr. Bishwajit/AAT-8147-2021
   Rokhum, Samuel Lalthazuala/L-8210-2013
   },
ORCID-Numbers = {Rokhum, Samuel Lalthazuala/0000-0001-8820-569X
   Kress, Thomas/0000-0001-9133-4310},
Funding-Acknowledgement = {SERB, India {[}SB/EMEQ-076/2014, SB/FT/CS-103/2013]; UK EPSRC
   Underpinning Multi-User Equipment grant {[}EP/P030467/1]; Ernest
   Oppenheimer Fund (Cambridge)},
Funding-Text = {This work is supported by SERB, India (Fund No. SB/EMEQ-076/2014 and
   SB/FT/CS-103/2013). We acknowledge the UK EPSRC Underpinning Multi-User
   Equipment grant EP/P030467/1 and SAIF IIT Bombay, for analysis. SLR
   thanks the Director, NIT Silchar for study leave. T. K. thanks the
   Ernest Oppenheimer Fund (Cambridge). Thanks go also to Professor Melinda
   J. Duer and Drs. David G. Reid and Heather Greer for help with data
   acquisition. In line with the requirements of UK Research \& Innovation,
   Open Data associated with this publication will be made available at the
   University of Cambridge data repository (see
   https://doi.org/10.17863/CAM.78670).},
Number-of-Cited-References = {77},
Times-Cited = {19},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {24},
Journal-ISO = {Renew. Energy},
Doc-Delivery-Number = {0C3GJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000775205500012},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001100049700001,
Author = {Puigdevall, Pau and Jerber, Julie and Danecek, Petr and Castellano,
   Sergi and Kilpinen, Helena},
Title = {Somatic mutations alter the differentiation outcomes of iPSC-derived
   neurons},
Journal = {CELL GENOMICS},
Year = {2023},
Volume = {3},
Number = {4},
Month = {APR 12},
Abstract = {The use of induced pluripotent stem cells (iPSC) as models for
   development and human disease has enabled the study of otherwise
   inaccessible tissues. A remaining challenge in developing reliable
   models is our limited understanding of the factors driving irregular
   differentiation of iPSCs, particularly the impact of acquired somatic
   mutations. We leveraged data from a pooled dopaminergic neuron
   differentiation experiment of 238 iPSC lines profiled with single-cell
   RNA and whole-exome sequencing to study how somatic mutations affect
   differentiation outcomes. We found that deleterious somatic mutations in
   key developmental genes, notably the BCOR gene, are strongly associated
   with failure in dopaminergic neuron differentiation and a larger
   proliferation rate in culture. We further identified broad differences
   in cell type composition between incorrectly and successfully
   differentiating lines, as well as significant changes in gene expression
   contributing to the inhibition of neurogenesis. Our work calls for
   caution in interpreting differentiation-related phenotypes in
   disease-modeling experiments.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Puigdevall, P; Kilpinen, H (Corresponding Author), UCL, UCL Great Ormond St Inst Child Hlth, 30 Guilford St, London WC1N 1EH, England.
   Kilpinen, H (Corresponding Author), Wellcome Sanger Inst, Wellcome Genome Campus, Hinxton CB10 1SA, Cambs, England.
   Puigdevall, P; Kilpinen, H (Corresponding Author), Univ Helsinki, Helsinki Inst Life Sci HILIFE, Haartmaninkatu 8,POB 63, Helsinki 00014, Finland.
   Kilpinen, H (Corresponding Author), Univ Helsinki, Fac Biol \& Environm Sci, Viikinkaari 1,POB 65, Helsinki 00014, Finland.
   Puigdevall, Pau; Castellano, Sergi; Kilpinen, Helena, UCL, UCL Great Ormond St Inst Child Hlth, 30 Guilford St, London WC1N 1EH, England.
   Jerber, Julie, Open Targets, Wellcome Genome Campus, Hinxton CB10 1SA, Cambs, England.
   Danecek, Petr; Kilpinen, Helena, Wellcome Sanger Inst, Wellcome Genome Campus, Hinxton CB10 1SA, Cambs, England.
   Puigdevall, Pau; Kilpinen, Helena, Univ Helsinki, Helsinki Inst Life Sci HILIFE, Haartmaninkatu 8,POB 63, Helsinki 00014, Finland.
   Kilpinen, Helena, Univ Helsinki, Fac Biol \& Environm Sci, Viikinkaari 1,POB 65, Helsinki 00014, Finland.},
DOI = {10.1016/j.xgen.2023.100280},
Article-Number = {100280},
ISSN = {2666-979X},
Keywords-Plus = {PLURIPOTENT STEM-CELLS; GENETIC-VARIATION; PROLIFERATION; CYCLE},
Research-Areas = {Cell Biology; Genetics \& Heredity},
Web-of-Science-Categories  = {Cell Biology; Genetics \& Heredity},
Author-Email = {pau.puigdevall@helsinki.fi
   helena.kilpinen@helsinki.fi},
Affiliations = {University of London; University College London; Wellcome Trust Sanger
   Institute; University of Helsinki; University of Helsinki},
ORCID-Numbers = {Kilpinen, Helena/0000-0001-6692-6154
   Puigdevall Costa, Pau/0000-0002-8687-4942},
Funding-Acknowledgement = {UK Medical Research Council {[}MR/L016311/1]; MRC eMedLab Medical
   Bioinformatics career development award; Helsinki Institute of Life
   Science; NIHR GOSH BRC},
Funding-Text = {This work was funded by the UK Medical Research Council (MR/L016311/1;
   MRC eMedLab Medical Bioinformatics career development award to H.K.) ,
   Helsinki Institute of Life Science (H.K.) , the ICH CIO (S.C. and P.P.)
   and the NIHR GOSH BRC (S.C., P.P., and H.K.) . The views expressed are
   those of the author (s) and not necessarily those of the NHS, the NIHR,
   or the Depart-ment of Health. The authors acknowledge Zenodo, the data
   repository devel-oped under the European Open Science Infrastructure
   (OpenAIRE) to facilitate the open access to our metadata and normalized
   gene count matrices. The au-thors gratefully acknowledge Drs. Daniel
   Gaffney, Oliver Stegle, and Florian Merkle for early access to the
   dopaminergic neuron single-cell dataset, and Drs. Daniel Seaton and Anna
   Cuomo for assistance with the DA data. The au-thors also acknowledge
   Drs. Matthew Hurles, Sebastian Gerety, and Osama Arshad for their
   feedback on the project. Illustration in Figures 1 and S4C and the
   graphical abstract were created with BioRender.com .},
Number-of-Cited-References = {59},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Cell Genom.},
Doc-Delivery-Number = {X7EX0},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001100049700001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000393586300115,
Author = {Kar, Arik and Sain, Sumanta and Rossouw, David and Knappett, Benjamin R.
   and Pradhan, Swapan Kumar and Botton, Gianluigi A. and Wheatley, Andrew
   E. H.},
Title = {Targeting low-cost type-II heterostructures: Synthesis, structure and
   photoreactivity},
Journal = {JOURNAL OF ALLOYS AND COMPOUNDS},
Year = {2017},
Volume = {698},
Pages = {944-956},
Month = {MAR 25},
Abstract = {One design strategy by which to iterate the photocatalytic efficiency of
   semiconducting nanomaterials for harvesting solar energy involves the
   synthesis of type-II heterostructured materials. In this article, a
   straightforward, facile and environmentally benign route to
   heterostructures in which SnO2 nanospheres are capped by PbS nanocubes
   is reported. It offers to address current limitations to photocatalytic
   efficiency brought about by electron-hole recombination and narrow
   photoresponsive ranges in many existing systems. PbS nanocubes are grown
   in the presence of preformed SnO2 nanospheres by functionalizing the
   surface of the latter using cetyltrimethylammonium bromide (CTAB).
   Heterostructure formation is confirmed by X-ray diffraction (XRD), Raman
   spectroscopy, X-ray photoelectron spectroscopy (XPS),
   Brunauer-Emmett-Teller (BET) surface area analysis, and transmission
   electron microscopy (TEM) analysis. Rietveld refinement has been
   exploited to simultaneously elucidate the atomic and microstructures of
   these materials, allowing the quantitative determination of particle
   structure and stability. The combination of narrow band-gap
   semiconductor (PbS) and wide band-gap semiconductor (SnO2) endows the
   heterostructured nanomaterial with potential as a photocatalyst and, in
   the degradation of Rhodamine B(RhB) dye under solar simulation, it
   showed superior photocatalytic activity to that of its separate SnO2 and
   PbS components. A strong type-II interaction is demonstrated by the
   heterostructure and a charge separation mechanism has been utilized to
   clarify this behaviour. (C) 2016 The Authors. Published by Elsevier B.V.},
Publisher = {ELSEVIER SCIENCE SA},
Address = {PO BOX 564, 1001 LAUSANNE, SWITZERLAND},
Type = {Article},
Language = {English},
Affiliation = {Kar, A; Wheatley, AEH (Corresponding Author), Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England.
   Kar, Arik; Knappett, Benjamin R.; Wheatley, Andrew E. H., Univ Cambridge, Dept Chem, Lensfield Rd, Cambridge CB2 1EW, England.
   Sain, Sumanta; Pradhan, Swapan Kumar, Univ Burdwan, Div Mat Sci, Dept Phys, Burdwan 713104, W Bengal, India.
   Rossouw, David; Botton, Gianluigi A., McMaster Univ, Dept Mat Sci \& Engn, Brockhouse Inst Mat Res, Hamilton, ON L8S 4L8, Canada.
   Rossouw, David; Botton, Gianluigi A., McMaster Univ, Canadian Ctr Electron Microscopy, Hamilton, ON L8S 4L8, Canada.},
DOI = {10.1016/j.jallcom.2016.12.167},
ISSN = {0925-8388},
EISSN = {1873-4669},
Keywords = {SnO2 nanosphere; PbS nanocube; Rietveld refinement; Heterostructure;
   Photochemistry},
Keywords-Plus = {ENHANCED PHOTOCATALYTIC ACTIVITY; SNO2 NANOPARTICLES; PHOTOLUMINESCENCE
   PROPERTIES; HETEROJUNCTION; NANOCRYSTALS; COMPOSITES; REFINEMENT;
   NANOWIRES; NANORODS; SURFACE},
Research-Areas = {Chemistry; Materials Science; Metallurgy \& Metallurgical Engineering},
Web-of-Science-Categories  = {Chemistry, Physical; Materials Science, Multidisciplinary; Metallurgy \&
   Metallurgical Engineering},
Author-Email = {ak899@cam.ac.uk},
Affiliations = {University of Cambridge; University of Burdwan; McMaster University;
   McMaster University},
ResearcherID-Numbers = {Sain, Sumanta/ABB-5440-2021
   PRADHAN, SUNIL KUMAR/E-2915-2016
   },
ORCID-Numbers = {PRADHAN, SUNIL KUMAR/0000-0003-1615-6168
   Sain, Sumanta/0000-0001-9229-8219
   Rossouw, David/0000-0003-2991-1812},
Funding-Acknowledgement = {Royal Society's Newton International Fellowship scheme {[}NF130808]; UK
   EPSRC {[}EP/J500380/1]; Royal Society {[}NF130808] Funding Source: Royal
   Society},
Funding-Text = {A. K. acknowledges support from the Royal Society's Newton International
   Fellowship scheme (NF130808). B. R. K. thanks the UK EPSRC for financial
   support (EP/J500380/1). Thanks go also to Drs. Tim Jones and Jill Geddes
   of Schlumberger Gould Research for help with the acquisition of Raman
   and X-ray photoelectron spectra, to Dr. Zlatko Saracevic of the
   Department of Chemical Engineering and Biotechnology (University of
   Cambridge) for help with BET surface area analysis, and to Mr. Tom
   Jellicoe for help with the photoluminescence measurements. Open Data for
   this paper are available at the University of Cambridge data repository
   (https://doi.org/10.17863/CAM.6905).},
Number-of-Cited-References = {62},
Times-Cited = {17},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {27},
Journal-ISO = {J. Alloy. Compd.},
Doc-Delivery-Number = {EJ9ZO},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000393586300115},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:001052160700001,
Author = {Wade, Natasha E. and McCabe, Connor J. and Wallace, Alexander L. and
   Gonzalez, Marybel R. and Hoh, Eunha and Infante, M. Alejandra and Mejia,
   Margie Hernandez and Haist, Frank},
Title = {Clouding Up Cognition? Secondhand Cannabis and Tobacco Exposure Related
   to Cognitive Functioning in Youth},
Journal = {BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE},
Year = {2023},
Volume = {3},
Number = {2},
Pages = {233-242},
Month = {APR},
Abstract = {BACKGROUND: Increasing legalization of cannabis, in addition to
   longstanding rates of tobacco use, raises con-cerns for possible
   cognitive decrements from secondhand smoke or environmental exposure,
   although little research exists. We investigate the relation between
   cognition and secondhand and environmental cannabis and tobacco exposure
   in youth.METHODS: The Adolescent Brain Cognitive Development (ABCD)
   Study year 2 follow-up (N = 5580; 48\% female) cognitive performance and
   secondhand or environmental cannabis or tobacco exposure data were used.
   Principal components analysis identified a global cognition factor.
   Linear mixed-effects models assessed global cognition and individual
   cognitive task performance by cannabis and/or tobacco environmental
   exposure. Sociodemographics and other potential confounds were examined.
   p values were adjusted using the false discovery rate method.RESULTS:
   Global cognition was not related to any exposure group after testing
   corrections and considering con-founds. Beyond covariates and family-and
   site-level factors, secondhand tobacco was related to poorer visual
   memory (p = .02), and environmental tobacco was associated with poorer
   visuospatial (p = .02) and language (p = .008) skills. Secondhand
   cannabis was related to cognition, but not after controlling for
   potential confounders (p . .05). Environmental cannabis was related to
   better oral reading (p = .01). Including covariates attenuated effect
   sizes. CONCLUSIONS: Secondhand tobacco exposure was associated with
   poorer visual memory, while environmental tobacco exposure was related
   to poorer language and visuospatial skills. Secondhand cannabis was not
   related to cognition after controlling for sociodemographic factors, but
   environmental cannabis exposure was related to better reading. Because,
   to our knowledge, this is the first known study of its kind and thus
   preliminary, secondhand cannabis should continue to be investigated to
   confirm results.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Wade, NE (Corresponding Author), Univ Calif San Diego, Dept Psychiat, La Jolla, CA 92093 USA.
   Wade, Natasha E.; Gonzalez, Marybel R.; Infante, M. Alejandra; Haist, Frank, Univ Calif San Diego, Dept Psychiat, La Jolla, CA 92093 USA.
   Hoh, Eunha, San Diego State Univ, Sch Publ Hlth, San Diego, CA USA.
   Mejia, Margie Hernandez, Univ Calif San Diego, San Diego State Univ, Joint Doctoral Program Clin Psychol, San Diego, CA USA.
   Wallace, Alexander L., Univ Wisconsin Milwaukee, Dept Psychol, Waukee, WI USA.
   McCabe, Connor J., Univ Washington, Dept Psychiat \& Behav Sci, Seattle, WA USA.},
DOI = {10.1016/j.bpsgos.2022.01.010},
EarlyAccessDate = {APR 2023},
ISSN = {2667-1743},
Keywords-Plus = {NONSMOKER EXPOSURE; SMOKE EXPOSURE; MARIJUANA; ALCOHOL; ASSOCIATIONS;
   ADOLESCENT},
Research-Areas = {Neurosciences \& Neurology; Psychiatry},
Web-of-Science-Categories  = {Neurosciences; Psychiatry},
Author-Email = {nwade@health.ucsd.edu},
Affiliations = {University of California System; University of California San Diego;
   California State University System; San Diego State University;
   University of California System; University of California San Diego;
   California State University System; San Diego State University;
   University of Wisconsin System; University of Wisconsin Milwaukee;
   University of Washington; University of Washington Seattle},
ORCID-Numbers = {Wade, Natasha/0000-0002-9629-2305
   Hoh, Eunha/0000-0002-4075-040X},
Funding-Acknowledgement = {National Institutes of Health (NIH) {[}U01DA041048, U01DA050989,
   U01DA051016, U01DA041022, U01DA051018, U01DA051037, U01DA050987,
   U01DA041174, U01DA041106, U01DA041117, U01DA041028, U01DA041134,
   U01DA050988, U01DA051039, U01DA041156, U01DA041025, U01DA041120,
   U01DA051038, U01DA041148, U01DA041093, U01DA041089, U24DA041123,
   U24DA041147];  {[}K08 DA050779];  {[}T32AA013525];  {[}T32AA007455]},
Funding-Text = {Data used in the preparation of this article were obtained from the ABCD
   Study (https://abcdstudy.org), held in the National Institute of Mental
   Health Data Archive. This is a multisite, longitudinal study designed to
   recruit more than 10,000 children aged 9 to 10 and follow them over 10
   years into early adulthood. The ABCD Study is supported by the National
   Institutes of Health (NIH) and additional federal partners (Grant Nos.
   U01DA041048,U01DA050989, U01DA051016, U01DA041022, U01DA051018,
   U01DA051037, U01DA050987, U01DA041174, U01DA041106,U01DA041117,
   U01DA041028, U01DA041134, U01DA050988,U01DA051039, U01DA041156,
   U01DA041025, U01DA041120,U01DA051038, U01DA041148, U01DA041093,
   U01DA041089,U24DA041123, and U24DA041147).A full list of supporters is
   available athttps://abcdstudy.org/federal-partners.html. A listing of
   participating sites and a complete listing of the study investigators
   can be found athttps://abcdstudy.org/consortium\_members/. ABCD
   consortium investigators designed and implemented the study and/or
   provided data but did not necessarily participate in analysis or writing
   of this report. This manuscript reflects the views of the authors and
   may not reflect the opinions or views of the National Institutes of
   Health or ABCD consortium investigators. The ABCD data repository grows
   and changes over time. The ABCD data used in this report came from ABCD
   Release 3.0 (DOI:10.15154/1519007).This work was also supported by Grant
   Nos. K08 DA050779 (principal investigator {[}PI], NEW), T32AA013525 (PI,
   Edward Riley), and T32AA007455(PI, Mary E. Larimer).The authors report
   no biomedical financial interests or potential conflicts of interest.},
Number-of-Cited-References = {61},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Biol. Psychiatr.-Glob. Open Sci.},
Doc-Delivery-Number = {P7AK0},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001052160700001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000339711000040,
Author = {Barbour, Andrew J. and Wyatt, Frank K.},
Title = {Modeling strain and pore pressure associated with fluid extraction: The
   Pathfinder Ranch experiment},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH},
Year = {2014},
Volume = {119},
Number = {6},
Pages = {5254-5273},
Month = {JUN},
Abstract = {Strainmeters can be subject to hydrologic effects from pumping of nearby
   water wells, depending on the state of the local rock. Strain signals
   associated with hydrology are generally not used and regarded as
   troublesome because they are much larger than most tectonic signals (e.
   g., tides or slow slip episodes in Cascadia), but here we show that
   fluid extraction leads to detectable strain and pore pressure signals,
   which we use to constrain valuable material properties of the rock,
   namely the hydraulic diffusivity and elastic shear modulus. We collected
   multiple years of pump activity at two active water wells near a pair of
   Plate Boundary Observatory borehole strainmeters in southern California.
   These data demonstrate clearly the connection between fluid extraction
   and deformation: the onset of transient strains and pore pressures is
   strongly correlated with both the onset of fluid extraction, and the
   sizes of the transient signals are strongly correlated with cumulative
   extraction volumes. These data also suggest that the instruments are a
   possible tool for remote monitoring of fluid injection and withdrawal.
   Based on poroelastic modeling, we find estimates of hydraulic
   diffusivity (0.061 m(2) s(-1) to 0.126 m(2) s(-1)) which are consistent
   with data for fractured igneous rock, and estimates of shear modulus
   (39.7 MPa to 101 MPa) which are comparable to data for shallow
   granodiorite-expected to be weak from weathering, and other sources of
   damage (e. g., faulting). We infer that crustal rock in this region is
   drained at shallow depths by pervasive, hydraulically conductive
   fractures: as a result of changes in applied stress, fluid flow will
   occur rather than a sustained change in pore fluid pressure.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Barbour, AJ (Corresponding Author), Univ Calif San Diego, Scripps Inst Oceanog, Inst Geophys \& Planetary Phys, La Jolla, CA 92093 USA.
   Barbour, Andrew J.; Wyatt, Frank K., Univ Calif San Diego, Scripps Inst Oceanog, Inst Geophys \& Planetary Phys, La Jolla, CA 92093 USA.},
DOI = {10.1002/2014JB011169},
ISSN = {2169-9313},
EISSN = {2169-9356},
Keywords-Plus = {FAULT GOUGE; PERMEABILITY; DEFORMATION; POROELASTICITY; CRYSTALLINE;
   EARTHQUAKES; SUBSIDENCE; INJECTION; RESERVOIR; STRESS},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {abarbour@ucsd.edu},
Affiliations = {University of California System; University of California San Diego;
   Scripps Institution of Oceanography},
ResearcherID-Numbers = {Barbour, Andrew/AAE-8172-2020},
ORCID-Numbers = {Barbour, Andrew/0000-0002-6890-2452},
Funding-Acknowledgement = {NSF {[}EAR10-53208]; Directorate For Geosciences; Division Of Earth
   Sciences {[}1251568] Funding Source: National Science Foundation},
Funding-Text = {We thank Duncan Agnew for numerous discussions, and assistance with data
   on the elastic properties of rock; Don Elliott for field assistance,
   Rongjiang Wang for making his poroelasticity modeling code available to
   us, and the administrative staff of the Pathfinder Ranch for being
   receptive and accommodating. Stewart Jewell has been especially helpful,
   and his enthusiasm is greatly appreciated. Dave Mencin, Mike Gottlieb,
   and Wade Johnson provided invaluable insight into finer workings of the
   instruments. Critical reviews by the Associate Editor, by Michael Manga,
   and by an anonymous reviewer improved the quality of this work. Support
   from NSF grant EAR10-53208 enabled this study, and the well-pumping data
   sets have been added to an Open Access data repository {[}Barbour,
   2013].},
Number-of-Cited-References = {68},
Times-Cited = {20},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {19},
Journal-ISO = {J. Geophys. Res.-Solid Earth},
Doc-Delivery-Number = {AM2WG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000339711000040},
DA = {2024-01-15},
}

@article{ WOS:000708132500001,
Author = {Lenz, Matthias and Lenz, Marlene M. and Andreev, Andrei and Scheidt,
   Stephanie and Gromig, Raphael and Lebas, Elodie and Fedorov, Grigory and
   Krastel, Sebastian and Melles, Martin and Wagner, Bernd},
Title = {Climate and environmental history at Lake Levinson-Lessing, Taymyr
   Peninsula, during the last 62 kyr},
Journal = {JOURNAL OF QUATERNARY SCIENCE},
Year = {2022},
Volume = {37},
Number = {5, SI},
Pages = {836-850},
Month = {JUL},
Abstract = {The 45.95 m-long sediment succession shown in core Co1401 from Lake
   Levinson-Lessing allows the reconstruction of the largely unexplored
   environmental and climatic history of the Taymyr Peninsula of the past
   62 kyr. The core was analysed with a multidisciplinary approach
   including lithological, granulometric, geochemical and pollen analyses.
   The proxy data indicate a relatively stable, herb-dominated environment
   with only subtle changes between a cold/wet late Marine Isotope Stage
   (MIS) 4 and early MIS 3, mild/dry middle and late MIS 3 and a cold/dry
   MIS 2. The absence of pronounced climate fluctuations demonstrates that
   the Lake Levinson-Lessing catchment was not covered by an ice sheet
   during this period. Changes in precipitation were likely caused by
   waxing and waning of the large Eurasian ice sheets outside of the Taymyr
   Peninsula, which changed the eastward moisture transport and atmospheric
   circulation patterns. MIS 1 at Lake Levinson-Lessing was associated with
   overall warmer and wetter conditions and short-term climate fluctuations
   during the Bolling-Allerod warming, Younger Dryas cooling and Preboreal
   transition, which indicates the influence of North Atlantic air masses.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Lenz, M (Corresponding Author), Univ Cologne, Inst Geol \& Mineral, Cologne, Germany.
   Lenz, Matthias; Lenz, Marlene M.; Andreev, Andrei; Scheidt, Stephanie; Gromig, Raphael; Melles, Martin; Wagner, Bernd, Univ Cologne, Inst Geol \& Mineral, Cologne, Germany.
   Andreev, Andrei, Alfred Wegener Inst Polar \& Marine Res, Res Unit Potsdam, Potsdam, Germany.
   Andreev, Andrei, Kazan Fed Univ, Kazan, Russia.
   Lebas, Elodie; Krastel, Sebastian, Univ Kiel, Inst Geosci, Kiel, Germany.
   Lebas, Elodie, Univ Paris, Inst Phys Globe Paris, Paris, France.
   Fedorov, Grigory, St Petersburg State Univ, St Petersburg, Russia.
   Fedorov, Grigory, Arctic \& Antarctic Res Inst, St Petersburg, Russia.},
DOI = {10.1002/jqs.3384},
EarlyAccessDate = {OCT 2021},
ISSN = {0267-8179},
EISSN = {1099-1417},
Keywords = {Arctic Russia; Lake Levinson-Lessing; multiproxy analyses; sediment
   record; Taymyr Peninsula},
Keywords-Plus = {POLAR URAL MOUNTAINS; ICE-MARGINAL ZONE; LATE PLEISTOCENE; ARCTIC
   RUSSIA; PALEOENVIRONMENTAL HISTORY; LEVEL FLUCTUATIONS; VEGETATION
   HISTORY; SEVERNAYA ZEMLYA; GLACIAL MAXIMUM; POLLEN RECORD},
Research-Areas = {Physical Geography; Geology},
Web-of-Science-Categories  = {Geography, Physical; Geosciences, Multidisciplinary},
Author-Email = {matthias.lenz@uni-koeln.de},
Affiliations = {University of Cologne; Helmholtz Association; Alfred Wegener Institute,
   Helmholtz Centre for Polar \& Marine Research; Kazan Federal University;
   University of Kiel; Universite Paris Cite; Saint Petersburg State
   University; Arctic \& Antarctic Research Institute},
ResearcherID-Numbers = {Fedorov, Grigory/N-5788-2019
   Wagner, Bernd/J-4682-2012
   Melles, Martin/J-4070-2012
   Andreev, Andrei A/J-2701-2015
   Krastel, Sebastian/C-2001-2017
   },
ORCID-Numbers = {Fedorov, Grigory/0000-0003-2269-4501
   Wagner, Bernd/0000-0002-1369-7893
   Melles, Martin/0000-0003-0977-9463
   Andreev, Andrei A/0000-0002-8745-9636
   Krastel, Sebastian/0000-0002-5899-9748
   Scheidt, Stephanie/0000-0002-9370-2700
   Gromig, Raphael/0000-0001-9217-4259
   Lebas, Elodie/0000-0003-1617-143X
   Lenz (nee Baumer), Marlene Margit/0000-0002-5352-3900},
Funding-Acknowledgement = {German Federal Ministry for Education and Research, BMBF {[}03G0859A,
   03F0830A]; Russian Science Foundation {[}20-17-00135]; Projekt DEAL;
   Russian Science Foundation {[}20-17-00135] Funding Source: Russian
   Science Foundation},
Funding-Text = {We are grateful to various colleagues from the University of Bergen and
   St. Petersburg State University for their expertise and logistical help
   during the coring campaign in spring 2017. We thank Nicole Mantke and
   Dorothea Klinghardt from the University of Cologne for assistance and
   help with the laboratory work. Financial support for this study was
   provided by the German Federal Ministry for Education and Research,
   BMBF, grant numbers 03G0859A ('PLOT-Project') and 03F0830A
   ('PLOT-Synthesis'). The work of A. Andreev was partly supported by the
   Russian Science Foundation, grant number 20-17-00135. The authors
   declare no conflicts of interest. All data will be accessible in the
   Pangaea data repository after publication. Open Access funding enabled
   and organized by Projekt DEAL.},
Number-of-Cited-References = {117},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {7},
Journal-ISO = {J. Quat. Sci.},
Doc-Delivery-Number = {3B0RA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000708132500001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:001122187400001,
Author = {Joseph, Merin and Read, Daniel J. and Rucklidge, Alastair M.},
Title = {Design of Linear Block Copolymers and <i>ABC</i> Star Terpolymers That
   Produce Two Length Scales at Phase Separation},
Journal = {MACROMOLECULES},
Year = {2023},
Volume = {56},
Number = {19},
Pages = {7847-7859},
Month = {SEP 26},
Abstract = {Quasicrystals (materials with long-range order but without the usual
   spatial periodicity of crystals) were discovered in several soft matter
   systems in the last 20 years. The stability of quasicrystals has been
   attributed to the presence of two prominent length scales in a specific
   ratio, which is 1.93 for the 12-fold quasicrystals most commonly found
   in soft matter. We propose design criteria for block copolymers such
   that quasicrystal-friendly length scales emerge at the point of phase
   separation from a melt, basing our calculations on the Random Phase
   Approximation. We consider two block copolymer families: linear chains
   containing two different monomer types in blocks of different lengths,
   and ABC star terpolymers. In all examples, we are able to identify
   parameter windows with the two length scales having a ratio of 1.93. The
   models that we consider that are simplest for polymer synthesis are,
   first, a monodisperse A(L)BA(S)B melt and, second, a model based on
   random reactions from a mixture of A(L), A(S), and B chains: both
   feature the length scale ratio of 1.93 and should be relatively easy to
   synthesize.},
Publisher = {AMER CHEMICAL SOC},
Address = {1155 16TH ST, NW, WASHINGTON, DC 20036 USA},
Type = {Article},
Language = {English},
Affiliation = {Joseph, M; Read, DJ; Rucklidge, AM (Corresponding Author), Univ Leeds, Sch Math, Leeds LS2 9JT, England.
   Joseph, Merin; Read, Daniel J.; Rucklidge, Alastair M., Univ Leeds, Sch Math, Leeds LS2 9JT, England.},
DOI = {10.1021/acs.macromol.3c00800},
EarlyAccessDate = {SEP 2023},
ISSN = {0024-9297},
EISSN = {1520-5835},
Keywords-Plus = {FARADAY WAVES; MICROPHASE SEPARATION; QUASI-CRYSTALS; FRANK-KASPER;
   PATTERNS; MORPHOLOGIES; STABILITY; SCATTERING; ORDER},
Research-Areas = {Polymer Science},
Web-of-Science-Categories  = {Polymer Science},
Author-Email = {fsmj@leeds.ac.uk
   D.J.Read@leeds.ac.uk
   A.M.Rucklidge@leeds.ac.uk},
Affiliations = {University of Leeds},
ResearcherID-Numbers = {Read, Daniel/O-6450-2019
   Rucklidge, Alastair Michael/E-9046-2011
   },
ORCID-Numbers = {Read, Daniel/0000-0003-1194-9273
   Rucklidge, Alastair Michael/0000-0003-2985-0976
   JOSEPH, MERIN/0000-0002-0441-9365},
Funding-Acknowledgement = {Engineering and Physical Sciences Research Council {[}EP/L015536/1];
   Soft Matter and Functional Interfaces (SOFI) Centre for Doctoral
   Training; School of Mathematics, University of Leeds {[}EP/P015611/1];
   Engineering and Physical Sciences Research Council {[}RF-2018-449/9,
   10.5518/1333]; Leverhulme Trust},
Funding-Text = {The authors thank Profs Andrew Archer, Ron Lifshitz, An-Chang Shi, and
   Bart Vorselaars for stimulating conversations, and Joanna Tumelty for
   advice on numerical methods. MJ is grateful for a PhD studentship from
   the Soft Matter and Functional Interfaces (SOFI) Centre for Doctoral
   Training (EP/L015536/1) and the School of Mathematics, University of
   Leeds. AMR is grateful for support from the Engineering and Physical
   Sciences Research Council (EP/P015611/1) and the Leverhulme Trust
   (RF-2018-449/9). The data associated with this paper are openly
   available from the University of Leeds Data Repository (10.5518/1333).
   For the purpose of open access, the authors have applied a Creative
   Commons Attribution (CC BY) license to any Author Accepted Manuscript
   version arising from this submission.},
Number-of-Cited-References = {73},
Times-Cited = {0},
Usage-Count-Last-180-days = {9},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Macromolecules},
Doc-Delivery-Number = {AZ8C2},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001122187400001},
OA = {hybrid, Green Published, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001122643300001,
Author = {McEntee, S. C. and Jackman, C. M. and Weigt, D. M. and Louis, C. K. and
   Dunn, W. R. and Boudouma, A. and Connerney, J. E. P. and Kurth, W. S.
   and Kraft, R. and Branduardi-Raymont, G. and Gladstone, G. R. and
   Rutala, M. J.},
Title = {Long Exposure Chandra X-Ray Observation of Jupiter\&apos;s Auroral
   Emissions During Juno Plasmasheet Encounters in September 2021},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2023},
Volume = {128},
Number = {12},
Month = {DEC},
Abstract = {On 15 September 2021, Chandra carried out a 40-hr (similar to 4 jovian
   rotations) observation as part of its longest planetary campaign to
   study the drivers of jovian X-ray aurora that may be linked to ultra-low
   frequency (ULF) wave activity. During this time, Juno's orbit had taken
   the spacecraft into Jupiter's dusk magnetosphere. Here is believed to be
   the most probable location of ULF waves propagating along jovian
   magnetic field lines that drive the X-ray auroral emissions. This is the
   first time that this region has been observed by an orbiter since
   Galileo >20 years ago, and never before has there been contemporaneous
   in situ and X-ray observations. A 1D solar wind propagation model
   identifies a compression event near the midpoint of the 40-hr
   observation window. The influence of a compression is confirmed when
   comparing the measured magnetic field in the dusk lobes of the
   magnetotail from Juno MAG data against a baseline lobe field model. Data
   from the Juno Waves instrument also show activation of broadband
   kilometric (bKOM) emissions during the arrival of the shock, a feature
   that has previously been observed during compression events. Therefore
   this is the first time we can fully analyze the morphological
   variability during the evolution of a shock. Wavelet transforms and
   Rayleigh testing are used to search for statistically significant
   quasi-periodic pulsations (QPPs) of the X-ray emissions in the data set,
   and find significant QPPs with periods of 25-26 min for the northern
   auroral X-rays.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {McEntee, SC (Corresponding Author), Dublin Inst Adv Studies, Sch Cosm Phys, DIAS Dunsink Observ, Dublin, Ireland.
   McEntee, SC (Corresponding Author), Trinity Coll Dublin, Sch Phys, Dublin, Ireland.
   McEntee, S. C.; Jackman, C. M.; Louis, C. K.; Rutala, M. J., Dublin Inst Adv Studies, Sch Cosm Phys, DIAS Dunsink Observ, Dublin, Ireland.
   McEntee, S. C., Trinity Coll Dublin, Sch Phys, Dublin, Ireland.
   Weigt, D. M., Aalto Univ, Dept Comp Sci, Aalto, Finland.
   Dunn, W. R., UCL, Dept Phys \& Astron, London, England.
   Dunn, W. R., UCL Birkbeck, Ctr Planetary Sci, London, England.
   Boudouma, A., PSL Res Univ, LESIA, Observ Paris, CNRS, Meudon, France.
   Connerney, J. E. P., Space Res Corp, Annapolis, MD USA.
   Kurth, W. S., Univ Iowa, Dept Phys \& Astron, Iowa City, IA USA.
   Kraft, R., Harvard Smithsonian Ctr Astrophys, Smithsonian Astrophys Observ, Cambridge, MA USA.
   Branduardi-Raymont, G., Univ Coll London, Dept Space \& Climate Phys, Mullard Space Sci Lab, Dorking, England.
   Gladstone, G. R., Southwest Res Inst, Space Sci \& Engn Div, San Antonio, TX USA.
   Gladstone, G. R., Univ Texas San Antonio, Dept Phys \& Astron, San Antonio, TX USA.
   WISA, Midrand, South Africa.},
DOI = {10.1029/2023JA031901},
Article-Number = {e2023JA031901},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords = {Jupiter; X-ray; Juno; magnetosphere; aurora; radio},
Keywords-Plus = {SOLAR-WIND; XMM-NEWTON; RADIO; MAGNETOPAUSE; WAVES; OSCILLATIONS;
   PULSATIONS; GALILEO; FIELD},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {mcentees@cp.dias.ie},
Affiliations = {Dublin Institute for Advanced Studies; Trinity College Dublin; Aalto
   University; University of London; University College London; University
   of London; University College London; Birkbeck University London;
   Universite Paris Cite; Centre National de la Recherche Scientifique
   (CNRS); Sorbonne Universite; Universite PSL; Observatoire de Paris;
   University of Iowa; Harvard University; Smithsonian Astrophysical
   Observatory; Smithsonian Institution; University of London; University
   College London; Southwest Research Institute; University of Texas
   System; University of Texas at San Antonio (UTSA)},
Funding-Acknowledgement = {Science Foundation Ireland; European Research Council (ERC) under the
   European Union {[}101101005]; STFC {[}ST/S000240/1]; Ernest Rutherford
   Fellowship {[}ST/W003449/1]; NASA {[}699041X]; Roy J. Carver Charitable
   Trust;  {[}18/FRL/6199]},
Funding-Text = {SCM's, CMJ's, MJR's, and CKL's work at DIAS was supported by Science
   Foundation Ireland award 18/FRL/6199. DMW work at Aalto University is
   funded from the European Research Council (ERC) under the European
   Union's Horizon 2020 research and innovation programme (project
   ``SYCOS{''}, Grant 101101005). WRD and GBR acknowledge support from STFC
   consolidated Grant ST/S000240/1 to University College London (UCL). WRD
   is supported by Ernest Rutherford Fellowship: ST/W003449/1. The research
   at the University of Iowa is supported by NASA through Contract 699041X
   with the Southwest Research Institute. WSK acknowledges the use of the
   Space Physics Data Repository at the University of Iowa supported by the
   Roy J. Carver Charitable Trust. Open access funding provided by IReL.},
Number-of-Cited-References = {86},
Times-Cited = {0},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {CA9J4},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001122643300001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000374730900035,
Author = {Nishiyama, Takanori and Miyoshi, Yoshizumi and Katoh, Yuto and Sakanoi,
   Takeshi and Kataoka, Ryuho and Okano, Shoichi},
Title = {Substructures with luminosity modulation and horizontal oscillation in
   pulsating patch: Principal component analysis application to pulsating
   aurora},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2016},
Volume = {121},
Number = {3},
Pages = {2360-2373},
Month = {MAR},
Abstract = {We observed a mesoscale aurora (100 km x 100km) with patchy structure
   and equatorward propagation at Poker Flat Research Range on 1 December
   2011. Fast Fourier transform (FFT) analysis revealed that this pulsating
   patch clearly exhibited temporal variations that can be categorized into
   two types: on-off pulsation (7.8-10s) with large amplitudes and
   luminosity modulations excited during on phase with a frequency of about
   3.0Hz. In addition, we applied principal component analysis (PCA) to
   time series image data of the pulsating aurora for the first time. Time
   coefficients were estimated by PCA for the whole patch and the
   substructures were consistent with those obtained from the FFT analysis,
   and therefore, we concluded that PCA is capable of decomposing several
   structures that have different coherent spatiotemporal characteristics.
   Another new insight in this study is that the rapid variations were
   highly localized; they were excited in only the substructures embedded
   in the whole structure. Moreover, the whole patch propagated equatorward
   because of ExB drift of cold plasma, while the substructures did not
   show such systematic propagation but rather forward-backward
   oscillations. The horizontal scale of the substructures was estimated to
   be no smaller than 410km at the magnetic equator, which is comparable to
   that of the wave packet structure of a whistler mode chorus
   perpendicular to the field line. We suggest that the apparent horizontal
   oscillation of the substructures is associated with field-aligned
   propagations of the whistler mode chorus in a duct.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Nishiyama, T (Corresponding Author), Natl Inst Polar Res, Tokyo, Japan.
   Nishiyama, T (Corresponding Author), Grad Univ Adv Studies, SOKENDAI, Dept Polar Sci, Tokyo, Japan.
   Nishiyama, Takanori; Kataoka, Ryuho, Natl Inst Polar Res, Tokyo, Japan.
   Nishiyama, Takanori; Kataoka, Ryuho, Grad Univ Adv Studies, SOKENDAI, Dept Polar Sci, Tokyo, Japan.
   Miyoshi, Yoshizumi, Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi 4648601, Japan.
   Katoh, Yuto, Tohoku Univ, Grad Sch Sci, Dept Geophys, Sendai, Miyagi 980, Japan.
   Sakanoi, Takeshi; Okano, Shoichi, Tohoku Univ, Grad Sch Sci, Planetary Plasma \& Atmospher Res Ctr, Sendai, Miyagi 980, Japan.},
DOI = {10.1002/2015JA022288},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords = {pulsating aurora; ground-based observations; wave-particle interactions;
   whistler mode chorus; small-scale aurora},
Keywords-Plus = {FINE-STRUCTURE; ELECTRONS; MECHANISM; CHORUS; WAVES; SPECTRA},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {nishiyama.takanori@nipr.ac.jp},
Affiliations = {Research Organization of Information \& Systems (ROIS); National
   Institute of Polar Research (NIPR) - Japan; Graduate University for
   Advanced Studies - Japan; Nagoya University; Tohoku University; Tohoku
   University},
ResearcherID-Numbers = {Nishiyama, Takanori/ABA-2671-2020
   Nishiyama, Takanori/D-5546-2016
   Miyoshi, Yoshizumi/T-5748-2019
   Katoh, Yuto/B-8007-2015
   Sakanoi, Takeshi/C-5593-2018
   KATAOKA, RYUHO/AAJ-4570-2020
   Miyoshi, Yoshizumi/B-5834-2015},
ORCID-Numbers = {Nishiyama, Takanori/0000-0002-3648-6589
   Nishiyama, Takanori/0000-0002-3648-6589
   Miyoshi, Yoshizumi/0000-0001-7998-1240
   Katoh, Yuto/0000-0002-4318-0633
   Sakanoi, Takeshi/0000-0002-7146-9020
   Miyoshi, Yoshizumi/0000-0001-7998-1240},
Funding-Acknowledgement = {Ministry of Education, Science, Sports, Technology, and Culture of Japan
   {[}K1232151, 25302006, 15H05815, 15H05747]; Institute for Space-Earth
   Environmental Research, Nagoya University; Global COE program Global
   Education and Research Center for Earth and Planetary Dynamics of Tohoku
   University; NIPR; Grants-in-Aid for Scientific Research {[}25302006,
   26302005, 15H03730] Funding Source: KAKEN},
Funding-Text = {We thank Dr. Donald L. Hampton, B. Lawson, K. Abnett, and all the staff
   of the Poker Flat Research Range for their helpful support during the
   observations. A. Otomo has supported us when we were making our
   ground-based observations at the Poker Flat Research Range in 2011-2012,
   and the authors appreciate her cooperation in this study. This work was
   carried out with funding from Grants-in-Aid for Japan Society for the
   Promotion of Science (JSPS) Fellows (K1232151) and Grants-in-Aid for
   Scientific Research (25302006, 15H05815, and 15H05747) from the Ministry
   of Education, Science, Sports, Technology, and Culture of Japan. This
   study was also supported by the joint research program of the Institute
   for Space-Earth Environmental Research, Nagoya University and the Global
   COE program Global Education and Research Center for Earth and Planetary
   Dynamics of Tohoku University. The production of this paper was
   supported by an NIPR publication subsidy. The IMF and solar wind data
   were obtained from the GSFC/SPDF OMNIWeb interface at
   http://omniweb.gsfc.nasa.gov/. The Dst and AE indices were provided by
   the World Data Center for Geomagnetism (WDC-C2) at Kyoto University.
   Ground-based magnetometer data were provided by the Geophysical
   Institute Magnetometer Array operated by the Geophysical Institute,
   University of Alaska, and they are available through the open data
   repository at UC Berkeley at http://themis.ssl.berkeley.edu/index.shtml.
   Aurora data were obtained from the EMCCD camera, all-sky camera, and
   photometer at the Poker Flat Research Range and are stored at the
   following address: http://polaris.nipr.ac.jp/similar to
   nishiyama/tmp/PFRR/.},
Number-of-Cited-References = {51},
Times-Cited = {10},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {8},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {DK2FV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000374730900035},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:001112806900001,
Author = {Evanski, Julia M. and Zundel, Clara G. and Baglot, Samantha L. and
   Desai, Shreya and Gowatch, Leah C. and Ely, Samantha L. and Sadik,
   Nareen and Lundahl, Leslie H. and Hill, Matthew N. and Marusak, Hilary
   A.},
Title = {The First ``Hit{''} to the Endocannabinoid System? Associations Between
   Prenatal Cannabis Exposure and Frontolimbic White Matter Pathways in
   Children},
Journal = {BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE},
Year = {2024},
Volume = {4},
Number = {1},
Pages = {11-18},
Month = {JAN},
Abstract = {BACKGROUND: Cannabis is the most used federally illicit substance among
   pregnant people in the United States. However, emerging preclinical data
   show that a significant portion of cannabis constituents, such as
   D9-tetrahydrocannabinol and its bioactive metabolites, readily cross the
   placenta and accumulate in the fetal brain, disrupting neurodevelopment.
   Recent research using the Adolescent Brain Cognitive Development (ABCD)
   Study cohort has linked prenatal cannabis exposure (PCE) to greater
   neurobehavioral problems and lower total gray and white matter volume in
   children. Here, we examined the impact of PCE on frontolimbic white
   matter pathways that are critical for cognitive- and emotion-related
   functioning, show a high density of cannabinoid receptors, and are
   susceptible to cannabis exposure during other periods of rapid
   neurodevelopment (e.g., adolescence).METHODS: This study included 11,530
   children (mean +/- SD age = 118.99 +/- 7.49 months; 47\% female) from
   the ABCD Study cohort. Linear mixed-effects models were used to examine
   the effects of caregiver-reported PCE on fractional anisotropy of 10
   frontolimbic pathways (5 per hemisphere).RESULTS: PCE was associated
   with lower fractional anisotropy of the right (3 = -0.005, p , .001) and
   left (3 = -0.003, p = .007) fornix, and these results remained
   significant after adjusting for a variety of covariates, multiple
   comparisons, fractional anisotropy of all fibers, and using a
   quality-control cohort only.CONCLUSIONS: In sum, we demonstrated small,
   yet reliable, effects of PCE on white matter integrity during childhood,
   particularly in the fornix, which plays a crucial role in emotion- and
   memory-related processes. Future studies are needed to understand the
   impacts of small changes in brain structure or function on
   neurodevelopment and risk of neurobehavioral problems.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Marusak, HA (Corresponding Author), Univ Calgary, Hotchkiss Brain Inst, Calgary, AB, Canada.
   Marusak, HA (Corresponding Author), Educ Univ Calgary, Mathison Ctr Mental Hlth Res, Calgary, AB, Canada.
   Marusak, HA (Corresponding Author), Wayne State Univ, Sch Med, Dept Pharmacol, Detroit, MI 48202 USA.
   Marusak, HA (Corresponding Author), Wayne State Univ, Merrill Palmer Skillman Inst Child \& Family Dev, Detroit, MI 48202 USA.
   Evanski, Julia M.; Zundel, Clara G.; Desai, Shreya; Gowatch, Leah C.; Ely, Samantha L.; Sadik, Nareen; Lundahl, Leslie H.; Marusak, Hilary A., Wayne State Univ, Sch Med, Dept Psychiat \& Behav Neurosci, Detroit, MI USA.
   Baglot, Samantha L.; Hill, Matthew N.; Marusak, Hilary A., Univ Calgary, Hotchkiss Brain Inst, Calgary, AB, Canada.
   Baglot, Samantha L.; Hill, Matthew N.; Marusak, Hilary A., Educ Univ Calgary, Mathison Ctr Mental Hlth Res, Calgary, AB, Canada.
   Marusak, Hilary A., Wayne State Univ, Sch Med, Dept Pharmacol, Detroit, MI 48202 USA.
   Marusak, Hilary A., Wayne State Univ, Merrill Palmer Skillman Inst Child \& Family Dev, Detroit, MI 48202 USA.},
DOI = {10.1016/j.bpsgos.2023.09.005},
EarlyAccessDate = {NOV 2023},
ISSN = {2667-1743},
Keywords-Plus = {MARIJUANA USE; BRAIN; IMPACTS; MICROSTRUCTURE; ADOLESCENTS; RECEPTORS;
   PREGNANCY; INTEGRITY; WOMEN; FMRI},
Research-Areas = {Neurosciences \& Neurology; Psychiatry},
Web-of-Science-Categories  = {Neurosciences; Psychiatry},
Author-Email = {hmarusak@med.wayne.edu},
Affiliations = {Wayne State University; University of Calgary; Wayne State University;
   Wayne State University},
ResearcherID-Numbers = {Marusak, Hilary/AAB-3307-2022},
ORCID-Numbers = {Marusak, Hilary/0000-0002-0771-6795},
Funding-Acknowledgement = {National Institutes of Health {[}U01DA041048, U01DA050989, U01DA051016,
   U01DA041022, U01DA051018, U01DA051037, U01DA050987, U01DA041174,
   U01DA041106, U01DA041117, U01DA041028, U01DA041134, U01DA050988,
   U01DA051039, U01DA041156, U01DA041025, U01DA041120, U01DA051038,
   U01DA041148, U01DA041093, U01DA041089, U24DA041123, U24DA041147];
   National Institute of Mental Health {[}K01MH119241, R01MH132830]; Eunice
   Kennedy Shriver National Institute of Child Health and Human Development
   {[}R21HD105882]},
Funding-Text = {Data used in the preparation of this article were obtained from the
   Adolescent Brain Cognitive Development (ABCD) Study (https://abcdstudy.
   org) , held in the National Institute of Mental Health Data Archive.
   This is a multisite, longitudinal study designed to recruit more than
   10,000 children ages 9 to 10 years and follow them over 10 years into
   early adulthood. The ABCD Study is supported by the National Institutes
   of Health and additional federal partners (Grant Nos. U01DA041048,
   U01DA050989, U01DA051016, U01DA041022, U01DA051018, U01DA051037,
   U01DA050987, U01DA041174, U01DA041106, U01DA041117, U01DA041028,
   U01DA041134, U01DA050988, U01DA051039, U01DA041156, U01DA041025,
   U01DA041120, U01DA051038, U01DA041148, U01DA041093, U01DA041089,
   U24DA041123, and U24DA041147) .A full list of supporters is available at
   https://abcdstudy.org/federal-partners.html. A listing of participating
   sites and a complete listing of the study investigators can be found at
   https://abcdstudy.org/consortium\_ members/. This manuscript reflects
   the views of the authors and may not reflect the opinions or views of
   the National Institutes of Health or ABCD consortium investigators.The
   ABCD data repository grows and changes over time.The ABCD data used in
   this report came from https://doi.org/10.15154/1523041. HAM is supported
   by National Institute of Mental Health (Grant Nos. K01MH119241 and
   R01MH132830) and Eunice Kennedy Shriver National Institute of Child
   Health and Human Development (Grant No. R21HD105882) .JME and HAM
   conceptualized and designed the project. JME, HAM, and CGZ analyzed and
   interpreted the data. All authors critically revised the final version
   of the manuscript. ABCD consortium investigators designed and
   implemented the study and/or provided data but did not necessarily
   participate in the analysis or writing of this report.The authors report
   no biomedical financial interests or potential conflicts of interest.},
Number-of-Cited-References = {60},
Times-Cited = {0},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Biol. Psychiatr.-Glob. Open Sci.},
Doc-Delivery-Number = {Z5XS3},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001112806900001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:001115075900001,
Author = {Meca, Alan and Peraza, Julio A. and Riedel, Michael C. and Hale, Willie
   and Pettit, Jeremy W. and Musser, Erica D. and Salo, Taylor and
   Flannery, Jessica S. and Bottenhorn, Katherine L. and Dick, Anthony S.
   and Lobo, Rosario Pintos and Ucros, Laura M. and Greaves, Chelsea A. and
   Hawes, Samuel W. and Sanchez, Mariana and Gonzalez, Marybel R. and
   Sutherland, Matthew T. and Gonzalez, Raul and Laird, Angela R.},
Title = {Acculturative Orientations Among Hispanic/ Latinx Caregivers in the ABCD
   Study: Associations With Caregiver and Youth Mental Health and Youth
   Brain Function},
Journal = {BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE},
Year = {2023},
Volume = {3},
Number = {4},
Pages = {785-796},
Month = {OCT},
Abstract = {BACKGROUND: Population-based neuroscience offers opportunities to
   examine important but understudied sociocultural factors such as
   acculturation. Acculturation refers to the extent to which an individual
   retains their cultural heritage and/or adopts the receiving society's
   culture and is particularly salient among Hispanic/Latinx immigrants.
   Specific acculturative orientations have been linked to vulnerability to
   substance use, depression, and suicide and are known to influence family
   dynamics between caregivers and their children.METHODS: Using data from
   first-and second-generation Hispanic/Latinx caregivers in the Adolescent
   Brain Cognitive Development (ABCD) Study (N = 1057), we examined how
   caregivers' acculturative orientation affects their mental health, as
   well as the mental health and brain function of their children.
   Neuroimaging analyses focused on regions associated with self-and
   affiliation-based social processing (ventromedial prefrontal cortex,
   insula, and temporoparietal junction).RESULTS: We identified 2 profiles
   of caregiver acculturation: bicultural (retains heritage culture while
   adopting U.S. culture) and detached (discards heritage culture and
   rejects U.S. culture). Bicultural caregivers exhibited fewer
   internalizing and externalizing problems than detached caregivers;
   furthermore, youth exhibited similar internalizing effects across
   caregiver profiles. In addition, youth with bicultural caregivers
   displayed increased resting-state brain activity (i.e., fractional
   amplitude of low-frequency fluctuations and regional homogeneity) in the
   left insula, which has been linked to psychopathology; however,
   differences in long-range functional connectivity were not
   significant.CONCLUSIONS: Caregiver acculturation is an important
   familial factor that has been linked to significant differences in youth
   mental health and insula activity. Future work should examine
   sociocultural and neurodevelopmental changes across adolescence to
   assess health outcomes and determine whether localized, corticolimbic
   brain effects are ultimately translated into long-range connectivity
   differences.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Meca, A (Corresponding Author), Univ Texas San Antonio, Dept Psychol, San Antonio, TX 78249 USA.
   Meca, Alan; Hale, Willie, Univ Texas San Antonio, Dept Psychol, San Antonio, TX 78249 USA.
   Peraza, Julio A.; Riedel, Michael C.; Laird, Angela R., Florida Int Univ, Dept Phys, Miami, FL 33199 USA.
   Pettit, Jeremy W.; Musser, Erica D.; Salo, Taylor; Dick, Anthony S.; Lobo, Rosario Pintos; Hawes, Samuel W.; Sutherland, Matthew T.; Gonzalez, Raul, Florida Int Univ, Dept Psychol, Miami, FL USA.
   Flannery, Jessica S., Univ N Carolina, Dept Psychol \& Neurosci, Chapel Hill, NC USA.
   Bottenhorn, Katherine L., Univ Southern Calif, Dept Populat \& Publ Hlth Sci, Los Angeles, CA USA.
   Ucros, Laura M.; Greaves, Chelsea A., Florida Int Univ, Sch Integrated Sci \& Humanities, Miami, FL USA.
   Sanchez, Mariana, Florida Int Univ, Dept Hlth Promot \& Dis Prevent, Miami, FL USA.
   Gonzalez, Marybel R., Univ Calif San Diego, Dept Psychiat, San Diego, CA USA.},
DOI = {10.1016/j.bpsgos.2023.02.005},
EarlyAccessDate = {OCT 2023},
ISSN = {2667-1743},
Keywords-Plus = {SENSITIVE PERIOD; PSYCHOPATHOLOGY; ADOLESCENCE; IMMIGRANTS; IDENTITY;
   FAMILY; MODEL; SCALE; FMRI},
Research-Areas = {Neurosciences \& Neurology; Psychiatry},
Web-of-Science-Categories  = {Neurosciences; Psychiatry},
Author-Email = {alan.meca@UTSA.edu},
Affiliations = {University of Texas System; University of Texas at San Antonio (UTSA);
   State University System of Florida; Florida International University;
   State University System of Florida; Florida International University;
   University of North Carolina; University of North Carolina Chapel Hill;
   University of Southern California; State University System of Florida;
   Florida International University; State University System of Florida;
   Florida International University; University of California System;
   University of California San Diego},
ResearcherID-Numbers = {Meca, Alan/S-6317-2016
   Gonzalez, Raul/B-2289-2009},
ORCID-Numbers = {Sanchez, Mariana/0000-0001-7794-4200
   Sutherland, Matthew/0000-0002-6091-4037
   Dick, Anthony/0000-0001-9907-8155
   Meca, Alan/0000-0002-3272-7701
   Gonzalez, Raul/0000-0002-5431-4828},
Funding-Acknowledgement = {National Institutes of Health (NIH) {[}U01DA041156, R01DA041353]; NIH; 
   {[}U01DA041048]},
Funding-Text = {This work was supported by the National Institutes of Health (NIH)
   (Grant No. U01DA041156 {[}to ARL, MCR, ASD, MTS, SWH, MS, and RG] and
   Grant No. R01DA041353 {[}to ARL, MTS, and MCR] ) . The ABCD Study is
   supported by the NIH and additional federal partners under Grant Nos.
   U01DA041048, https://abcdstudy.org/federal-partners.html. ABCD
   Consortium in-vestigators designed and implemented the study and/or
   provided data but did not necessarily participate in the analysis or
   writing of this report. This manuscript reflects the views of the
   authors and may not reflect the opinions or views of the NIH or ABCD
   consortium investigators. AM and ARL conceived and designed the project.
   AM, JAP, MCR, WH, and ARL analyzed the data. JAP, MCR, TS, JSF, and KLB
   contributed scripts and pipelines. WH, ASD, and MTS provided statistical
   support. JWP, RPL, LMU, CAG, SWH, MS, MRG, and RG provided support for
   analysis of ABCD measures and results interpretation. AM, JAP, MCR, and
   ARL wrote the paper, and all authors contributed to the revisions and
   approved the final version. We thank the Florida International
   University Instructional \& Research Computing Center
   (http://ircc.fiu.edu) for providing the high performance cluster and
   computing resources that contributed to the research results reported in
   this paper. A previous version of this article was published as a
   preprint on bioRxiv: https://
   www.biorxiv.org/content/10.1101/2022.07.24.501248v2.article-info. Data
   used in the preparation of this article were obtained from the ABCD
   Study (https://abcdstudy.org) , held in the NDA. This is a multisite,
   longitu-dinal study designed to recruit more than 10,000 children ages 9
   to 10 years and follow them over 10 years into early adulthood. A
   listing of participating sites and a complete listing of the study
   investigators can be found at
   https://abcdstudy.org/consortium\_members/. The ABCD data repository
   grows and changes over time. The ABCD data used in this report came from
   NDA ABCD Release 3.0 (https://doi. org/10.15154/1520591) . An NDA study
   was created to associate the ana-lyses reported in this study with the
   underlying ABCD Study data (https://doi.org/10.15154/1527751) .
   Additional information and resources are available on a project page for
   this study at the Open Science Framework (https://osf.io/mkdw3/) . The
   code is available in 2 GitHub repositories, including one for analysis
   of the Vancouver Index of Acculturation data (https://github.com
   /NBCLab/abcd-hispanic-via) and one for the fMRI pre-processing and
   analyses (https://github.com /NBCLab/abcd\_fmriprep-analysis) . Regions
   of interest and connectivity maps are available in Neu-roVault
   (https://identifiers.org/neurovault.collection:1276) . High-resolution},
Number-of-Cited-References = {91},
Times-Cited = {2},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Biol. Psychiatr.-Glob. Open Sci.},
Doc-Delivery-Number = {Z9GE7},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001115075900001},
OA = {Green Submitted, gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000827434400001,
Author = {Di Girolamo, P. and De Rosa, B. and Summa, D. and Franco, N. and
   Veselovskii, I},
Title = {Measurements of Aerosol Size and Microphysical Properties: A Comparison
   Between Raman Lidar and Airborne Sensors},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-ATMOSPHERES},
Year = {2022},
Volume = {127},
Number = {14},
Month = {JUL 27},
Abstract = {This manuscript compares measurements of aerosol size distributions and
   microphysical properties retrieved from the Raman lidar BASIL with those
   obtained from a series of aircraft sensors during HyMeX-SOP1. The
   attention is focused on a measurement session on 02 October 2012, with
   BASIL measurements revealing the presence of a lower aerosol layer
   extending up to 3.3 km and an elevated layer extending from 3.6 to 4.6
   km. Aerosol size distribution and microphysical properties are
   determined from multi-wavelength particle backscattering and extinction
   profile measurements through a retrieval approach based on Tikhonov
   regularization. A good agreement is found between BASIL and the
   microphysical sensors' measurements for all considered aerosol size and
   microphysical properties. Specifically, BASIL and in-situ volume
   concentration values are in the range 2-5 mu m(3) cm(-3) in the lower
   layer and in the range 1-3.5 mu m(3) cm(-3) in the upper layer. Values
   of the effective radius values from BASIL and the in-situ sensors are in
   the range 0.2-0.6 mu m in both the lower and upper layer. Aerosol size
   distributions are determined at 2.2, 2.8, 4 and 4.3 km, with a good
   agreement between the Raman lidar and the microphysical sensors at all
   considered heights. We combined these size and microphysical results
   with Lagrangian back-trajectory analyses and chemical composition
   measurements. From this combination of datasets we conclude that aerosol
   particles below 3 km were probably originated by wildfires in North
   America and/or by anthropogenic activities in North-Eastern Europe,
   while aerosols above 3 km were also probably originated by wildfires in
   North America.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Di Girolamo, P (Corresponding Author), Univ Basilicata, Scuola Ingn, Potenza, Italy.
   Di Girolamo, P.; De Rosa, B.; Summa, D.; Franco, N., Univ Basilicata, Scuola Ingn, Potenza, Italy.
   De Rosa, B.; Summa, D., CNR, Ist Metodol Anal Ambientale, Tito, Italy.
   Veselovskii, I, Russian Acad Sci, Prokhorov Gen Phys Inst, Moscow, Russia.},
DOI = {10.1029/2021JD036086},
Article-Number = {e2021JD036086},
ISSN = {2169-897X},
EISSN = {2169-8996},
Keywords = {aerosol; effective radius; wildfires; size distribution; refractive
   index; aerosol type and origin; aerosol size and microphysical
   properties; Raman lidar; in-situ microphysical and chemical sensors;
   back-trajectory analysis},
Keywords-Plus = {INTER-COMPARISON EFFORT; MEDITERRANEAN EXPERIMENT; TROPOSPHERIC AEROSOL;
   CLOUD MICROPHYSICS; HYDROLOGICAL CYCLE; OPTICAL-PROPERTIES; SAHARAN
   DUST; EXTINCTION; PERFORMANCE; INVERSION},
Research-Areas = {Meteorology \& Atmospheric Sciences},
Web-of-Science-Categories  = {Meteorology \& Atmospheric Sciences},
Author-Email = {paolo.digirolamo@unibas.it},
Affiliations = {University of Basilicata; Consiglio Nazionale delle Ricerche (CNR);
   Istituto di Metodologie per l'Analisi Ambientale (IMAA-CNR); Russian
   Academy of Sciences; Prokhorov General Physics Institute of the Russian
   Academy of Sciences},
ORCID-Numbers = {Summa, Donato/0000-0002-0867-4144
   DI GIROLAMO, Paolo/0000-0002-7420-3164},
Funding-Acknowledgement = {Grants MISTRALS/HyMeX; IODA-MED project {[}ANR-11-BS56-0005]; Italian
   Ministry for Education, University and Research; Italian Space Agency;
   Russian Science Foundation {[}21-17-00114]; Universita degli Studi della
   Basilicata within the CRUI-CARE Agreement},
Funding-Text = {Wind Profiler dataset were collected in the frame of the HyMeX program,
   sponsored by Grants MISTRALS/HyMeX and ANR-11-BS56-0005 IODA-MED project
   (contact person: Frederique Said, Universite Toulouse-Laboratoire
   d'Aerologie, Toulouse, France). This work was supported by the Italian
   Ministry for Education, University and Research under the Grants STAC-UP
   and FISR2019-CONCERNING, and by the Italian Space Agency under the
   Grants As-ATLAS and CALIGOLA. Lidar retrieval algorithms were developed
   thanks to the support by Russian Science Foundation (project
   21-17-00114). The dataset used in the present research effort and the
   corresponding metadata are archived in the open public data repository
   HyMeX database, freely accessible through the link
   http://mistrals.sedoo.fr/HyMeX/.Open Access Funding provided by
   Universita degli Studi della Basilicata within the CRUI-CARE Agreement.},
Number-of-Cited-References = {75},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {11},
Journal-ISO = {J. Geophys. Res.-Atmos.},
Doc-Delivery-Number = {3A7KI},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000827434400001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:001052280100001,
Author = {Moreau, Allison L. and Voss, Michaela and Hansen, Isabella and Paul,
   Sarah E. and Barch, Deanna M. and Rogers, Cynthia E. and Bogdan, Ryan},
Title = {Prenatal Selective Serotonin Reuptake Inhibitor Exposure, Depression,
   and Brain Morphology in Middle Childhood: Results From the ABCD Study},
Journal = {BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE},
Year = {2023},
Volume = {3},
Number = {2},
Pages = {243-254},
Month = {APR},
Abstract = {BACKGROUND: Prenatal selective serotonin reuptake inhibitor (SSRI)
   exposure has been inconsistently linked to depression, and little is
   known about neural correlates. We examined whether prenatal SSRI
   exposure is associated with depressive symptoms and brain structure
   during middle childhood.METHODS: Prenatal SSRI exposure (retrospective
   caregiver report), depressive symptoms (caregiver-reported Child
   Behavior Checklist), and brain structure (magnetic resonance
   imaging-derived subcortical volume; cortical thickness and surface area)
   were assessed in children (analytic ns = 5420-7528; 235 with prenatal
   SSRI exposure; 9-10 years of age) who completed the baseline Adolescent
   Brain Cognitive Development Study session. Linear mixed-effects models
   nested data. Covariates included familial, pregnancy, and child
   variables. Matrix spectral decomposition adjusted for multiple
   testing.RESULTS: Prenatal SSRI exposure was not independently associated
   with depression after accounting for recent maternal depressive
   symptoms. Prenatal SSRI exposure was associated with greater left
   superior parietal surface area (b = 145.3 mm2, p = .00038) and lateral
   occipital cortical thickness (b = 0.0272 mm, p = .0000079); neither was
   associated with child depressive symptoms. Child depression was
   associated with smaller global brain structure.CONCLUSIONS: Our
   findings, combined with adverse outcomes of exposure to maternal
   depression and the utility of SSRIs for treating depression, suggest
   that risk for depression during middle childhood should not discourage
   SSRI use during pregnancy. Associations between prenatal SSRI exposure
   and brain structure were small in magnitude and not associated with
   depression. It will be important for future work to examine
   asso-ciations between prenatal SSRI exposure and depression through
   young adulthood, when risk for depression increases.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Moreau, AL; Bogdan, R (Corresponding Author), Washington Univ St Louis, Dept Psychol \& Brain Sci, St Louis, MO 63130 USA.
   Moreau, Allison L.; Voss, Michaela; Hansen, Isabella; Paul, Sarah E.; Barch, Deanna M.; Bogdan, Ryan, Washington Univ St Louis, Dept Psychol \& Brain Sci, St Louis, MO 63130 USA.
   Barch, Deanna M.; Rogers, Cynthia E., Washington Univ, Sch Med St Louis, Dept Psychiat, St Louis, MO USA.
   Barch, Deanna M., Washington Univ, Sch Med St Louis, Dept Radiol, St Louis, MO USA.},
DOI = {10.1016/j.bpsgos.2022.02.005},
EarlyAccessDate = {APR 2023},
ISSN = {2667-1743},
Keywords-Plus = {ANTIDEPRESSANT EXPOSURE; MATERNAL DEPRESSION; ANTENATAL DEPRESSION;
   MEDICATION USE; IN-UTERO; CHILDREN; PREGNANCY; BEHAVIOR;
   NEURODEVELOPMENT; OUTCOMES},
Research-Areas = {Neurosciences \& Neurology; Psychiatry},
Web-of-Science-Categories  = {Neurosciences; Psychiatry},
Author-Email = {amoreau@wustl.edu
   rbogdan@wustl.edu},
Affiliations = {Washington University (WUSTL); Saint Louis University; Washington
   University (WUSTL); Saint Louis University; Washington University
   (WUSTL)},
ORCID-Numbers = {Moreau, Allison/0000-0002-8758-8622},
Funding-Acknowledgement = {National Institutes of Health {[}U01DA050989, U01DA051016, U01DA041022,
   U01DA051018, U01DA051037, U01DA050987, U01DA041174, U01DA041106,
   U01DA041117, U01DA041028, U01DA041134, U01DA050988, U01DA051039,
   U01DA041156, U01DA041025, U01DA041120, U01DA051038, U01DA041148,
   U01DA041093, U01DA041089, U24DA041123, U24DA041147, R01-DA046224,
   R34-DA050272, R01-MH121877, R01-MH113570, R01-MH113883, R01-MH066031,
   U01- MH109589, U01 -A005020803, R01-MH090786, R01-AG045231,
   R01-HD083614, R01-AG052564, R21-AA027827];  {[}U01DA041048]},
Funding-Text = {Data used in the preparation of this article were obtained from the
   Adolescent Brain Cognitive Development (ABCD) Study (https://abcdstudy.
   org) , held in the NIMH Data Archive (NDA) . This is a multisite,
   longitudinal study designed to recruit more than 10,000 children ages
   9-10 and follow them over 10 years into early adulthood. The ABCD data
   repository grows and changes over time. The ABCD data used in this
   report came from NDA Study DOI: 10.15154/1524692. The ABCD Study is
   supported by the National Institutes of Health and additional federal
   partners under award numbers U01DA041048, U01DA050989, U01DA051016,
   U01DA041022, U01DA051018, U01DA051037, U01DA050987, U01DA041174,
   U01DA041106, U01DA041117, U01DA041028, U01DA041134, U01DA050988,
   U01DA051039, U01DA041156, U01DA041025, U01DA041120, U01DA051038,
   U01DA041148, U01DA041093, U01DA041089, U24DA041123, U24DA041147. A full
   list of supporters is available at
   https://abcdstudy.org/federal-partners.html. A listing of participating
   sites and a complete listing of the study investigators can be found at
   https://abcdstudy.org/consortium\_members/. ABCD consortium
   investigators designed and implemented the study and/or provided data
   but did not necessarily participate in the analysis or writing of this
   report. This manuscript reflects the views of the authors and may not
   reflect the opinions or views of the NIH or ABCD consortium
   investigators.This work was also supported by National Institutes of
   Health Grant Nos. R01-DA046224 (to CER) , R34-DA050272 (to CER) ,
   R01-MH121877 (to CER) , R01-MH113570 (to CER) , R01-MH113883 (to DMB) ,
   R01-MH066031 (to DMB) , U01- MH109589 (to DMB) , U01 -A005020803 (to
   DMB) , R01-MH090786 (to DMB) , R01-AG045231 (to RB) , R01-HD083614 (to
   RB) , R01-AG052564 (to RB) , R21-AA027827 (to RB) , and R01-DA046224 (to
   RB) . A previous version of this article was published as a preprint on
   medRxiv: https://medrxiv.org/content/10.1101/2021.09.01.21262980. The
   authors report no biomedical financial interests or potential conflicts
   of interest.},
Number-of-Cited-References = {58},
Times-Cited = {2},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {0},
Journal-ISO = {Biol. Psychiatr.-Glob. Open Sci.},
Doc-Delivery-Number = {P7EX7},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001052280100001},
OA = {Green Accepted, gold, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000416244200035,
Author = {Palma, Aniello and Artelsmair, Markus and Wu, Guanglu and Lu, Xiaoyong
   and Barrow, Steven J. and Uddin, Najib and Rosta, Edina and Masson, Eric
   and Scherman, Oren A.},
Title = {Cucurbit{[}7]uril as a Supramolecular Artificial Enzyme for Diels-Alder
   Reactions},
Journal = {ANGEWANDTE CHEMIE-INTERNATIONAL EDITION},
Year = {2017},
Volume = {56},
Number = {49},
Pages = {15688-15692},
Month = {DEC 4},
Abstract = {The ability to mimic the activity of natural enzymes using
   supramolecular constructs (artificial enzymes) is a vibrant scientific
   research field. Herein, we demonstrate that cucurbit{[}7]uril (CB{[}7])
   can catalyse Diels-Alder reactions for a number of substituted and
   unreactive N-allyl-2-furfurylamines under biomimetic conditions, without
   the need for protecting groups, yielding powerful synthons in previously
   unreported mild conditions. CB{[}7] rearranges the substrate in a highly
   reactive conformation and shields it from the aqueous environment,
   thereby mimicking the mode of action of a natural Diels-Alderase. These
   findings can be directly applied to the phenomenon of product inhibition
   observed in natural Diels-Alderase enzymes, and pave the way toward the
   development of novel, supramolecular-based green catalysts.},
Publisher = {WILEY-V C H VERLAG GMBH},
Address = {POSTFACH 101161, 69451 WEINHEIM, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Scherman, OA (Corresponding Author), Univ Cambridge, Dept Chem, Melville Lab Polymer Synth, Lensfield Rd, Cambridge CB2 1EW, England.
   Masson, E (Corresponding Author), Ohio Univ, Dept Chem \& Biochem, Athens, OH 45701 USA.
   Palma, Aniello; Artelsmair, Markus; Wu, Guanglu; Barrow, Steven J.; Scherman, Oren A., Univ Cambridge, Dept Chem, Melville Lab Polymer Synth, Lensfield Rd, Cambridge CB2 1EW, England.
   Lu, Xiaoyong; Masson, Eric, Ohio Univ, Dept Chem \& Biochem, Athens, OH 45701 USA.
   Uddin, Najib; Rosta, Edina, Kings Coll London, Dept Chem, London SE1 1DB, England.},
DOI = {10.1002/anie.201706487},
ISSN = {1433-7851},
EISSN = {1521-3773},
Keywords = {biomimetic catalysts; cucurbit{[}7]uril; Diels-Alder reactions; enzyme
   mimics},
Keywords-Plus = {OPENING METATHESIS POLYMERIZATION; DOMINO METATHESIS; COMPLEXES;
   EFFICIENT; PHOTODIMERIZATION; REGIOSELECTIVITY; DERIVATIVES;
   SELECTIVITY; CATALYSIS; OXIDATION},
Research-Areas = {Chemistry},
Web-of-Science-Categories  = {Chemistry, Multidisciplinary},
Author-Email = {masson@ohio.edu
   oas23@cam.ac.uk},
Affiliations = {University of Cambridge; University System of Ohio; Ohio University;
   University of London; King's College London},
ResearcherID-Numbers = {Lu, Xiaoyong/K-8229-2014
   Wu, Guanglu/AAI-4842-2020
   },
ORCID-Numbers = {Lu, Xiaoyong/0000-0002-8188-0569
   Wu, Guanglu/0000-0002-9690-5992
   Rosta, Edina/0000-0002-9823-4766
   Artelsmair, Markus/0000-0002-2516-2925
   Barrow, Steven/0000-0001-6417-1800},
Funding-Acknowledgement = {ERC {[}ASPiRe 240629]; EPSRC Programme Grant (NOtCH) {[}EP/L027151/1];
   Leverhulme Trust (Natural material innovation for sustainable living);
   European Commission {[}658360]; EPSRC {[}EP/N020669/1]; American
   Chemical Society Petroleum Research Fund (PRF) {[}51053-ND4]; EPSRC
   {[}EP/L027151/1, EP/N020669/1] Funding Source: UKRI; Engineering and
   Physical Sciences Research Council {[}EP/G060649/1, EP/N020669/1,
   EP/L027151/1] Funding Source: researchfish; Marie Curie Actions (MSCA)
   {[}658360] Funding Source: Marie Curie Actions (MSCA)},
Funding-Text = {O.A.S. and A.P. acknowledge an ERC starting investigator grant (ASPiRe
   240629) and EPSRC Programme Grant (NOtCH, EP/L027151/1) for the support,
   G.W. thanks the Leverhulme Trust (Natural material innovation for
   sustainable living) for the support, S.J.B. thanks the European
   Commission for a Marie Curie Fellowship (NANOSPHERE, 658360), E.R.
   gratefully acknowledges financial support from EPSRC (EP/N020669/1),
   E.M. and X.L. acknowledge the American Chemical Society Petroleum
   Research Fund (PRF No. 51053-ND4), the Department of Chemistry and
   Biochemistry, the College of Arts and Sciences and the Vice President
   for Research at Ohio University. Additional open data related to this
   publication is available at the University of Cambridge data repository
   (https://doi.org/10.17863/CAM.12345)},
Number-of-Cited-References = {41},
Times-Cited = {66},
Usage-Count-Last-180-days = {13},
Usage-Count-Since-2013 = {130},
Journal-ISO = {Angew. Chem.-Int. Edit.},
Doc-Delivery-Number = {FN8BR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED); Index Chemicus (IC)},
Unique-ID = {WOS:000416244200035},
OA = {Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001022266500007,
Author = {Fyfe, Laura-Jane and Underhill, John R.},
Title = {THE UPPER PERMIAN ZECHSTEIN SUPERGROUP OF NE ENGLAND AND THE ADJACENT
   SOUTHERN NORTH SEA: A REVIEW OF ITS ROLE IN THE UK'S ENERGY TRANSITION},
Journal = {JOURNAL OF PETROLEUM GEOLOGY},
Year = {2023},
Volume = {46},
Number = {3},
Pages = {383-406},
Month = {JUL},
Abstract = {As the United Kingdom reduces its CO2 emissions in order to meet its
   2050 net zero greenhouse gas targets, there will be a significant
   evolution of the UK's energy mix. The reliance on hydrocarbons will
   decrease while there is predicted to be an increase in low carbon energy
   sources such as renewables and nuclear. In order to decarbonise and
   achieve the net zero emissions targets while concurrently producing
   enough energy to provide for national energy needs, large-scale, low
   carbon energy generation projects need to be developed alongside energy
   storage facilities to provide flexibility within a low carbon energy
   supply. Robust CCUS programmes will need be developed in order to
   capture and store unavoidable carbon dioxide emissions. The subsurface
   geology of the UK provides opportunities for the development of low
   carbon energy generation, energy storage and CCS, and the Upper Permian
   Zechstein Supergroup deposited in eastern England and offshore in the
   Southern North Sea is a potential host for these new developments. In NE
   England, salt cavern gas storage sites have been developed in thick
   Zechstein evaporites since the mid 20th centrury. In this paper we
   present new isopach maps and well correlation panels which will help to
   outline optimal locations for the development of additional salt caverns
   for gas storage. A review of the Zechstein Supergroup indicates that it
   does not exhibit great potential for the development of CCS, due both to
   its complex reservoir characteristics and to difficulties with both
   subsurface imaging and monitoring. However thick Zechstein evaporites
   could provide an excellent seal for CO2 storage in the underlying Lower
   Permian Rotliegend Group.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Review},
Language = {English},
Affiliation = {Fyfe, LJ (Corresponding Author), Heriot Watt Univ, Edinburgh EH14 4AS, Scotland.
   Fyfe, Laura-Jane, Heriot Watt Univ, Edinburgh EH14 4AS, Scotland.
   Underhill, John R., Univ Aberdeen, Aberdeen AB24 3FX, Scotland.},
DOI = {10.1111/jpg.12843},
ISSN = {0141-6421},
EISSN = {1747-5457},
Keywords = {Zechstein Supergroup; Permian; Southern North Sea; England; Southern
   Permian Basin; energy transition; salt caverns},
Keywords-Plus = {SALT DEPOSITS; EXPLORATION; STORAGE},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {L.Fyfe@hw.ac.uk},
Affiliations = {Heriot Watt University; University of Aberdeen},
Funding-Acknowledgement = {Shell},
Funding-Text = {The authors thank Shell for sponsoring this research as well as the NAM
   team for insightful discussions. They thank Rachel Jamieson for her
   support, for interesting discussions and acknowledge the UK Onshore
   Geophysical Library (UKOGL) for their assistance in providing well data
   from their archives. IHS Markit are thanked for the provision of, and
   permission to publish, examples from their onshore well database. The UK
   National Data Repository (NDR) is gratefully acknowledged for access to
   the released UK offshore well database, as is the North Sea Transition
   Authority (NSTA) for access to their MegaMerge seismic survey. The
   British Geological Society (BGS) is thanked for use of online
   open-access datasets such as the geology of Britain viewer, offshore
   Geoindex and boreholes material database. The authors thank Kara
   English, Alun Williams and an anonymous referee for their insightful
   reviews.},
Number-of-Cited-References = {72},
Times-Cited = {2},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Pet. Geol.},
Doc-Delivery-Number = {L3JX0},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001022266500007},
DA = {2024-01-15},
}

@article{ WOS:001052286700001,
Author = {Jeong, Hee Jung and Moore, Tyler M. and Durham, E. Leighton and Reimann,
   Gabrielle E. and Dupont, Randolph M. and Cardenas-Iniguez, Carlos and
   Berman, Marc G. and Lahey, Benjamin B. and Kaczkurkin, Antonia N.},
Title = {General and Specific Factors of Environmental Stress and Their
   Associations With Brain Structure and Dimensions of Psychopathology},
Journal = {BIOLOGICAL PSYCHIATRY: GLOBAL OPEN SCIENCE},
Year = {2023},
Volume = {3},
Number = {3},
Pages = {480-489},
Month = {JUL},
Abstract = {BACKGROUND: Early-life stressors can adversely affect the developing
   brain. While hierarchical modeling has established the existence of a
   general factor of psychopathology, no studies have modeled a general
   factor of environmental stress and related this factor to brain
   development. Using a large sample of children from the ABCD (Adolescent
   Brain Cognitive Development) Study, the current study aimed to identify
   general and specific factors of environmental stress and test their
   associations with brain structure and psychopathology.METHODS: In a
   sample of 11,878 children, bifactor modeling and higher-order
   (second-order) modeling identified general and specific factors of
   environmental stress: family dynamics, interpersonal support,
   neighborhood socioeconomic status deprivation, and urbanicity.
   Structural equation modeling was performed to examine associations
   between these factors and regional gray matter volume (GMV) and cortical
   thickness as well as general and specific factors of
   psychopathology.RESULTS: The general environmental stress factor was
   associated with globally smaller cortical and subcortical GMV as well as
   thinner cortices across widespread regions. Family dynamics and
   neighborhood socioeconomic status deprivation were associated with
   smaller GMV in focal regions. Urbanicity was associated with larger
   cortical and subcortical GMV and thicker cortices in frontotemporal
   regions. The environmental factors were associated with psychopathology
   in the expected directions. The general factors of environmental stress
   and psychopathology were both predictors of smaller GMV in children,
   while remaining distinct from each other. CONCLUSIONS: This study
   reveals a unifying model of environmental influences that illustrates
   the inherent orga-nization of environmental stressors and their
   relationship to brain structure and psychopathology.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Kaczkurkin, AN (Corresponding Author), Vanderbilt Univ, Dept Psychol, Nashville, TN 37235 USA.
   Jeong, Hee Jung; Durham, E. Leighton; Reimann, Gabrielle E.; Dupont, Randolph M.; Kaczkurkin, Antonia N., Vanderbilt Univ, Dept Psychol, Nashville, TN 37235 USA.
   Moore, Tyler M., Univ Penn, Perelman Sch Med, Dept Psychiat, Philadelphia, PA USA.
   Cardenas-Iniguez, Carlos; Berman, Marc G., Univ Chicago, Dept Psychol, Chicago, IL USA.
   Lahey, Benjamin B., Univ Chicago, Dept Hlth Studies, Chicago, IL USA.
   Lahey, Benjamin B., Univ Chicago, Grossman Inst Neurosci, Quantitat Biol \& Human Behav MGB, Chicago, IL USA.
   Berman, Marc G., Univ Chicago, Grossman Inst Neurosci, Quantitat Biol \& Human Behav, Chicago, IL USA.
   Cardenas-Iniguez, Carlos, Univ Southern Calif, Keck Sch Med, Dept Populat \& Publ Hlth Sci, Los Angeles, CA USA.},
DOI = {10.1016/j.bpsgos.2022.04.004},
EarlyAccessDate = {JUL 2023},
ISSN = {2667-1743},
Keywords-Plus = {CHILDHOOD MALTREATMENT; CORTICAL THICKNESS; PATTERNS; CHILDREN; HEALTH},
Research-Areas = {Neurosciences \& Neurology; Psychiatry},
Web-of-Science-Categories  = {Neurosciences; Psychiatry},
Author-Email = {antonia.kaczkurkin@vanderbilt.edu},
Affiliations = {Vanderbilt University; University of Pennsylvania; University of
   Chicago; University of Chicago; University of Chicago; University of
   Chicago; University of Southern California},
Funding-Acknowledgement = {National Institute on Drug Abuse {[}UG3DA045251]; National Institute of
   Mental Health {[}R01MH098098, R01MH117014, R00MH117274, T32-MH18921];
   National Center for Advancing Translational Sciences {[}UL1TR000430,
   UL1TR000445]; NARSAD Young Investigator Award from the Brain and
   Behavior Research Foundation; Sloan Research Fellowship; Lifespan Brain
   Institute of the University of Pennsylvania; Children's Hospital of
   Philadelphia; National Institutes of Health {[}U01DA050989, U01DA051016,
   U01DA041022, U01DA051 018, U01DA051037, U01 DA05 0987, U01DA 041174,
   U01DA041106, U01 DA04 1117, U01DA0410 28, U01DA041134, U01DA050988, U01
   DA05 1039, U01DA0411 56, U01DA041025, U01DA041120, U01 DA05 1038,
   U01DA041093, U01DA041089, U24DA041123, U24DA041147, SCR\_015769]},
Funding-Text = {\& nbsp;This work was supported by the National Institute on Drug Abuse
   (Grant No. UG3DA045251 {[}to BBL] ) , National Institute of Mental
   Health (Grant Nos. R01MH098098 {[}to BBL] , R01MH117014 {[}to TMM] ,
   R00MH117274 {[}to ANK] , and T32-MH18921 {[}ELD is supported as a
   trainee on this grant] ) , National Center for Advancing Translational
   Sciences (Grant Nos. UL1TR000430 and UL1TR000445 {[}to BBL] ) , NARSAD
   Young Investigator Award from the Brain and Behavior Research Foundation
   (to ANK) , Sloan Research Fellowship (to ANK) , and Lifespan Brain
   Institute of the University of Pennsylvania and the Children's Hospital
   of Philadelphia (to TMM) . Data used in the preparation of this article
   were obtained from the ABCD Study (https://abcdstudy.org) , held in the
   National Institute of Mental Health Data Archive. This is a multisite,
   longitudinal study designed to recruit more than 10,000 children 9 to 10
   years of age and follow them over 10 years into early adulthood. The
   ABCD Study is supported by the National Institutes of Health and
   additional federal partners (Grant Nos. U01DA04104 8, U01DA050989,
   U01DA051016, U01DA041022, U01DA051 018, U01DA051037, U01 DA05 0987,
   U01DA 041174, U01DA041106, U01 DA04 1117, U01DA0410 28, U01DA041134,
   U01DA050988, U01 DA05 1039, U01DA0411 56, U01DA041025, U01DA041120, U01
   DA05 1038, U01DA0411 48, U01DA041093, U01DA041089, U24DA041123,
   U24DA041147) . A full list of supporters is available at
   https://abcdstudy.org/federal-partners.html. A list of participating
   sites and a complete list of the study investigators are available at
   https://abcdstudy.org/consortium\_members/. ABCD consortium
   investigators designed and implemented the study and/or provided data,
   but did not necessarily participate in the analysis or writing of this
   report. This article reflects the views of the authors and may not
   reflect the opinions or views of the National Institutes of Health or
   ABCD consortium investigators. The ABCD data repository grows and
   changes over time. The ABCD data used in this report came from ABCD
   Study data release 3.0 (RRID: SCR\_015769, DOI 10.15154/1520591) and
   National Institute of Mental Health Data Archive study DOI
   10.15154/1520063. DOIs can be found at https://nda.nih.gov/abcd/. The
   authors report no biomedical financial interests or potential conflicts
   of interest.},
Number-of-Cited-References = {45},
Times-Cited = {1},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {1},
Journal-ISO = {Biol. Psychiatr.-Glob. Open Sci.},
Doc-Delivery-Number = {P7FE0},
Web-of-Science-Index = {Emerging Sources Citation Index (ESCI)},
Unique-ID = {WOS:001052286700001},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000991004800001,
Author = {Ergintav, Semih and Floyd, Michael and Paradissis, Demitris and
   Karabulut, Hayrullah and Vernant, Philippe and Masson, Frederic and
   Georgiev, Ivan and Konca, Ali Ozgun and Dogan, Ugur and King, Robert and
   Reilinger, Robert},
Title = {New geodetic constraints on the role of faults and blocks versus
   distributed strain in the Nubia-Arabia-Eurasia zone of active plate
   interactions},
Journal = {TURKISH JOURNAL OF EARTH SCIENCES},
Year = {2023},
Volume = {32},
Number = {3, SI},
Pages = {248-261},
Abstract = {We present a broad view of present-day motions and deformations derived
   from uniform processing of GNSS observations within the
   Nubia-Arabia-Eurasia zone of plate interaction. The new observations we
   present provide a similar to 29\% increase in the number of velocity
   determinations, a reduction in average station spacing from similar to
   76 km to similar to 39 km, and an improvement in velocity uncertainties
   (for <1 mm/year), from 180 to 578 sites compared to our prior published
   solution (Reilinger et al., 2006). We use these new constraints to
   better evaluate the role of faults and blocks in controlling the
   character of continental deformation within the zone of plate
   interactions. Simple elastic block models show that internal deformation
   of the region occurs in large part on mapped, seismically active fault
   systems, indicating elastic behavior of the seismogenic crust (above
   similar to 15 km). For example, eastern central Anatolia, an area of >
   similar to 126,000 km(2), bounded by the North and East Anatolian Faults
   exhibits internal velocity differences of <0.5 mm/year, indicating
   strain rates of < similar to 1.5 nanostrain/year. Geodetically
   constrained fault slip rates obtained from this simplified approach are
   comparable to geologic rates, indicating that major faults have
   controlled the recent geologic evolution of the region (i.e. 5-10 Myr).
   The pattern of present-day deformation, including increasingly fast
   motions towards the Hellenic trench, and the roughly simultaneous
   opening of all the major Mediterranean basins in the early Miocene with
   the slowing of the Nubia-Eurasia convergence, support conceptual models
   that foundering and rollback of the subducted Nubian slab beneath the
   Aegean is the primary mechanism responsible for present-day motion and
   internal deformation of the Anatolian-Aegean region.},
Publisher = {Tubitak Scientific \& Technological Research Council Turkey},
Address = {ATATURK BULVARI NO 221, KAVAKLIDERE, TR-06100 ANKARA, TURKIYE},
Type = {Article},
Language = {English},
Affiliation = {Ergintav, S (Corresponding Author), Bogazici Univ, Dept Geodesy, Kandilli Observ, Istanbul, Turkiye.
   Ergintav, S (Corresponding Author), Bogazici Univ, Earthquake Res Inst, Istanbul, Turkiye.
   Ergintav, Semih, Bogazici Univ, Dept Geodesy, Kandilli Observ, Istanbul, Turkiye.
   Ergintav, Semih; Karabulut, Hayrullah; Konca, Ali Ozgun, Bogazici Univ, Earthquake Res Inst, Istanbul, Turkiye.
   Floyd, Michael; King, Robert; Reilinger, Robert, MIT, Dept Earth Atmospher \& Planetary Sci, Cambridge, MA USA.
   Paradissis, Demitris, Natl Tech Univ Athens, Dept Topog, Athens, Greece.
   Karabulut, Hayrullah; Konca, Ali Ozgun, Bogazici Univ, Dept Geophys, Kandilli Observ, Istanbul, Turkiye.
   Vernant, Philippe, Univ Montpellier, Geosci Lab, Montpellier, France.
   Masson, Frederic, Univ Strasbourg, Inst Phys Globe, Strasbourg, France.
   Georgiev, Ivan, Bulgarian Acad Sci, Natl Inst Geophys Geodesy \& Geog, Sofia, Bulgaria.
   Dogan, Ugur, Yildiz Tech Univ, Dept Geomat Engn, Istanbul, Turkiye.},
DOI = {10.55730/1300-0985.1842},
ISSN = {1300-0985},
Keywords = {Anatolia; Aegean; GNSS deformation; subduction; geodynamics;
   Mediterranean},
Keywords-Plus = {LATE CENOZOIC EVOLUTION; GPS MEASUREMENTS; ANATOLIAN FAULT; CORINTH
   RIFT; MIDDLE-EAST; DEFORMATION; DYNAMICS; TURKEY; KINEMATICS; SUBDUCTION},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {semih.ergintav@boun.edu.tr},
Affiliations = {Bogazici University; Bogazici University; Massachusetts Institute of
   Technology (MIT); National Technical University of Athens; Bogazici
   University; Universite de Montpellier; Universites de Strasbourg
   Etablissements Associes; Universite de Strasbourg; Bulgarian Academy of
   Sciences; Yildiz Technical University},
ResearcherID-Numbers = {Floyd, Michael/E-3766-2012
   Vernant, Philippe/C-9743-2010},
ORCID-Numbers = {Floyd, Michael/0000-0002-1657-2084
   Vernant, Philippe/0000-0001-5185-0070},
Funding-Acknowledgement = {Massachusetts Institute of Technology (MIT) International Science and
   Technology Initiatives (MISTI) {[}202048]; Scientific and Technological
   Research Council of Turkey (TUEBITAK) {[}114Y250]},
Funding-Text = {We gratefully acknowledge late Prof. Dr Aykut Barka (Istanbul Technical
   University) for initiating GPS-based geodynamic studies in Turkey, Dr
   Kim Kastens (Lamont-Doherty Geological Observatory) for leading early
   GPS investigations in the Aegean, and the many individuals and
   institutions that contributed to GNSS survey observations and maintained
   continuous GNSS stations in the Anatolian-Aegean region. This research
   was supported in part by Massachusetts Institute of Technology (MIT)
   International Science and Technology Initiatives (MISTI) Grant no:
   202048, and The Scientific and Technological Research Council of Turkey
   (TUEBITAK) Project no: 114Y250.We would like to thank the reviewers for
   the constructive suggestions as well as for their time to review the
   manuscript.We have used GNSS data that are in the public domain (UNAVCO,
   IGS, EUREF) and in the supplementary materials of the previously
   published studies and open data repositories. We also provide the
   calculated velocity fields, with respect to selected velocity reference
   frames in the Auxiliary Section of this manuscript.},
Number-of-Cited-References = {90},
Times-Cited = {0},
Usage-Count-Last-180-days = {6},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Turk. J. Earth Sci.},
Doc-Delivery-Number = {G7OJ4},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000991004800001},
DA = {2024-01-15},
}

@article{ WOS:000721033400001,
Author = {Liu, Yanliang and Guo, Jingsong and Xue, Yuhuan and Sangmanee,
   Chalermrat and Wang, Huiwu and Zhao, Chang and Khokiattiwong, Somkiat
   and Yu, Weidong},
Title = {Seasonal variation in diel vertical migration of zooplankton and
   micronekton in the Andaman Sea observed by a moored ADCP},
Journal = {DEEP-SEA RESEARCH PART I-OCEANOGRAPHIC RESEARCH PAPERS},
Year = {2022},
Volume = {179},
Month = {JAN},
Abstract = {The diel vertical migration (DVM) behaviors of zooplankton and
   micronekton vary among species in response to diverse ambient
   conditions. Based on the observed mean volumes of backscattering
   strength (MVBS), we studied the mean features and seasonal variations of
   DVM in the Andaman Sea. Nocturnal-ascent DVM pattern prevailed
   throughout the observation period, with a mean downward (upward)
   migratory speed of 3.85 (3.81) cm/s. The DVM in this area exhibited a
   3-layer vertical structure. Between the surface nighttime residence and
   the daytime residence below 300 m, there was a weak subsurface daytime
   residence probably formed by the assemblage of migrants avoiding aerobic
   predators. The variations in lower margin depth of surface nighttime
   residence and the upper margin depth of subsurface daytime residence
   were consistent with the variation in oxycline depth, which is closely
   related to thermocline variations. Compared with the premonsoon season,
   the MVBS was weaker, but the DVM was more active during the summer
   monsoon season, corresponding to the water clarity trend. Overall,
   equatorial Kelvin waves and monsoon winds presumably dominated the
   seasonal variations in DVM by modulating sea water properties such as
   oxygen concentration and transparency.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Liu, YL (Corresponding Author), Minist Nat Resources, Inst Oceanog 1, Qingdao 266061, Peoples R China.
   Liu, Yanliang; Guo, Jingsong; Xue, Yuhuan; Wang, Huiwu; Zhao, Chang, Minist Nat Resources, Key Lab Marine Sci \& Numer Modeling, Inst Oceanog 1, Qingdao 266061, Peoples R China.
   Liu, Yanliang, Qingdao Natl Lab Marine Sci \& Technol, Lab Reg Oceanog \& Numer Modeling, Qingdao 266237, Peoples R China.
   Liu, Yanliang, Shandong Key Lab Marine Sci \& Numer Modeling, Qingdao 266061, Peoples R China.
   Sangmanee, Chalermrat; Khokiattiwong, Somkiat, Phuket Marine Biol Ctr, Dept Marine \& Coastal Resources, Phuket, Thailand.
   Yu, Weidong, Sun Yat Sen Univ, Sch Atmospher Sci, Guangzhou, Guangdong, Peoples R China.},
DOI = {10.1016/j.dsr.2021.103663},
EarlyAccessDate = {NOV 2021},
Article-Number = {103663},
ISSN = {0967-0637},
EISSN = {1879-0119},
Keywords = {Diel vertical migration; Mean volumes of backscattering strength;
   Residence layer; Thermocline depth and oxycline depth; Water clarity;
   Kelvin wave; Monsoon},
Keywords-Plus = {OXYGEN MINIMUM ZONE; ADAPTIVE SIGNIFICANCE; SCATTERING LAYERS;
   SOUND-SCATTERING; INDIAN-OCEAN; VARIABILITY; BAY; PACIFIC; BIOMASS;
   CARBON},
Research-Areas = {Oceanography},
Web-of-Science-Categories  = {Oceanography},
Author-Email = {liuyl@fio.org.cn},
Affiliations = {Ministry of Natural Resources of the People's Republic of China; Laoshan
   Laboratory; Sun Yat Sen University},
ResearcherID-Numbers = {Yu, Weidong/IWL-8649-2023
   shi, danyang/ABG-6569-2021
   Yu, Weidong/I-7130-2013
   },
ORCID-Numbers = {Yu, Weidong/0000-0003-2503-2415
   Liu, Yanliang/0000-0002-3311-4560
   Khokiattiwong, Somkiat/0000-0003-3494-6569
   Sangmanee, Chalermrat/0000-0003-3664-5751},
Funding-Acknowledgement = {Marine S\&T Fund of Shandong Province {[}2018SDKJ0105-3]; Asian
   cooperation fund {[}99950410]; NSFC of China {[}41406034]},
Funding-Text = {This study was funded by the Marine S\&T Fund of Shandong Prov-ince for
   Pilot National Laboratory for Marine Science and Technology (Qingdao)
   (No.2018SDKJ0105-3) . This study was also supported by Asian cooperation
   fund 99950410 and NSFC grants 41406034 of China. This study was
   conducted under the framework of the regional inter-national cooperation
   project Monsoon Onset Monitoring and its Social and Ecosystem Impact
   (MOMSEI) and the Ocean Forecasting and Marine Disasters Mitigation
   System for Southeast Asia Seas (OFS) . The obser-vational data from the
   AS are available under the MOMSEI project in the Open Science Framework
   (OSF) data repository (https://osf.io/dash board) .},
Number-of-Cited-References = {63},
Times-Cited = {5},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {34},
Journal-ISO = {Deep-Sea Res. Part I-Oceanogr. Res. Pap.},
Doc-Delivery-Number = {XB0NK},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000721033400001},
DA = {2024-01-15},
}

@article{ WOS:000595466300001,
Author = {Gill, Dipender and Arvanitis, Marios and Carter, Paul and Cordero, Ana
   I. Hernandez and Jo, Brian and Karhunen, Ville and Larsson, Susanna C.
   and Li, Xuan and Lockhart, Sam M. and Mason, Amy and Pashos, Evanthia
   and Saha, Ashis and Tan, Vanessa Y. and Zuber, Verena and Bosse, Yohan
   and Fahle, Sarah and Hao, Ke and Jiang, Tao and Joubert, Philippe and
   Lunt, Alan C. and Ouwehand, Willem Hendrik and Roberts, David J. and
   Timens, Wim and van den Berge, Maarten and Watkins, Nicholas A. and
   Battle, Alexis and Butterworth, Adam S. and Danesh, John and Di
   Angelantonio, Emanuele and Engelhardt, Barbara E. and Peters, James E.
   and Sin, Don D. and Burgess, Stephen},
Title = {ACE inhibition and cardiometabolic risk factors, lung <i>ACE2</i> and
   <i>TMPRSS2</i> gene expression, and plasma ACE2 levels: a Mendelian
   randomization study},
Journal = {ROYAL SOCIETY OPEN SCIENCE},
Year = {2020},
Volume = {7},
Number = {11},
Month = {NOV 18},
Abstract = {Angiotensin-converting enzyme 2 (ACE2) and serine protease TMPRSS2 have
   been implicated in cell entry for severe acute respiratory syndrome
   coronavirus 2 (SARS-CoV-2), the virus responsible for coronavirus
   disease 2019 (COVID-19). The expression of ACE2 and TMPRSS2 in the lung
   epithelium might have implications for the risk of SARS-CoV-2 infection
   and severity of COVID-19. We use human genetic variants that proxy
   angiotensin-converting enzyme (ACE) inhibitor drug effects and
   cardiovascular risk factors to investigate whether these exposures
   affect lung ACE2 and TMPRSS2 gene expression and circulating ACE2
   levels. We observed no consistent evidence of an association of
   genetically predicted serum ACE levels with any of our outcomes. There
   was weak evidence for an association of genetically predicted serum ACE
   levels with ACE2 gene expression in the Lung eQTL Consortium (p =
   0.014), but this finding did not replicate. There was evidence of a
   positive association of genetic liability to type 2 diabetes mellitus
   with lung ACE2 gene expression in the Gene-Tissue Expression (GTEx)
   study (p = 4 x 10(-4)) and with circulating plasma ACE2 levels in the
   INTERVAL study (p = 0.03), but not with lung ACE2 expression in the Lung
   eQTL Consortium study (p = 0.68). There were no associations of
   genetically proxied liability to the other cardiometabolic traits with
   any outcome. This study does not provide consistent evidence to support
   an effect of serum ACE levels (as a proxy for ACE inhibitors) or
   cardiometabolic risk factors on lung ACE2 and TMPRSS2 expression or
   plasma ACE2 levels.},
Publisher = {ROYAL SOC},
Address = {6-9 CARLTON HOUSE TERRACE, LONDON SW1Y 5AG, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Burgess, S (Corresponding Author), Univ Cambridge, Med Res Council, Wellcome Trust Med Res Council Inst Metab Sci, Metab Dis Unit, Cambridge, England.
   Burgess, S (Corresponding Author), Univ Cambridge, Dept Publ Hlth \& Primary Care, British Heart Fdn, Cardiovasc Epidemiol Unit, Cambridge, England.
   Burgess, S (Corresponding Author), Univ Cambridge, Cambridge Inst Publ Hlth, Med Res Council, Biostat Unit, Cambridge, England.
   Burgess, S (Corresponding Author), Univ Cambridge, British Heart Fdn Ctr Res Excellence, Cambridge, England.
   Burgess, S (Corresponding Author), Univ Cambridge, Homerton Coll, Cambridge, England.
   Burgess, S (Corresponding Author), Uppsala Univ, Natl Inst Hlth Res, Cambridge Biomed Res Ctr, Cambridge, England.
   Gill, Dipender; Karhunen, Ville; Zuber, Verena; Lunt, Alan C., Imperial Coll London, St Marys Hosp, Dept Epidemiol \& Biostatist, Med Sch Bldg, London, England.
   Arvanitis, Marios, Johns Hopkins Univ, Div Cardiol, Dept Med, Baltimore, MD USA.
   Saha, Ashis, Johns Hopkins Univ, Dept Comp Sci, Baltimore, MD USA.
   Battle, Alexis, Johns Hopkins Univ, Dept Biomed Engn, Baltimore, MD USA.
   Battle, Alexis, Johns Hopkins Univ, Ctr Computat Biol, Baltimore, MD USA.
   Carter, Paul, Univ Cambridge, Dept Publ Hlth \& Primary Care, Cambridge, England.
   Lockhart, Sam M.; Burgess, Stephen, Univ Cambridge, Med Res Council, Wellcome Trust Med Res Council Inst Metab Sci, Metab Dis Unit, Cambridge, England.
   Mason, Amy; Fahle, Sarah; Jiang, Tao; Butterworth, Adam S.; Danesh, John; Di Angelantonio, Emanuele; Burgess, Stephen, Univ Cambridge, Dept Publ Hlth \& Primary Care, British Heart Fdn, Cardiovasc Epidemiol Unit, Cambridge, England.
   Zuber, Verena; Burgess, Stephen, Univ Cambridge, Cambridge Inst Publ Hlth, Med Res Council, Biostat Unit, Cambridge, England.
   Fahle, Sarah; Roberts, David J.; Watkins, Nicholas A.; Butterworth, Adam S.; Danesh, John; Di Angelantonio, Emanuele, Univ Cambridge, Natl Inst Hlth Res, Blood \& Transplant Res Unit Donor Hlth \& Genom, Cambridge, England.
   Butterworth, Adam S.; Danesh, John; Di Angelantonio, Emanuele; Burgess, Stephen, Univ Cambridge, British Heart Fdn Ctr Res Excellence, Cambridge, England.
   Burgess, Stephen, Univ Cambridge, Homerton Coll, Cambridge, England.
   Cordero, Ana I. Hernandez; Li, Xuan; Sin, Don D., Univ British Columbia, St Pauls Hosp, Ctr Heart Lung Innovat, Vancouver, BC, Canada.
   Jo, Brian, Lewis Sigler Inst Integrat Biol, Program Quantitat \& Computat Biol, Princeton, NJ USA.
   Larsson, Susanna C., Karolinska Inst, Unit Cardiovasc \& Nutr Epidemiol, Inst Environm Med, Stockholm, Sweden.
   Larsson, Susanna C., Uppsala Univ, Dept Surg Sci, Uppsala, Sweden.
   Mason, Amy; Fahle, Sarah; Butterworth, Adam S.; Danesh, John; Di Angelantonio, Emanuele; Burgess, Stephen, Uppsala Univ, Natl Inst Hlth Res, Cambridge Biomed Res Ctr, Cambridge, England.
   Mason, Amy; Fahle, Sarah; Butterworth, Adam S.; Danesh, John; Di Angelantonio, Emanuele; Burgess, Stephen, Cambridge Univ Hosp, Cambridge, England.
   Pashos, Evanthia, Pfizer Worldwide Res Dev \& Med, Internal Med Res Unit, Cambridge, MA USA.
   Tan, Vanessa Y., Univ Bristol, Med Res Council Integrat Epidemiol Unit, Bristol, Avon, England.
   Tan, Vanessa Y., Univ Bristol, Bristol Med Sch, Populat Hlth Sci, Bristol, Avon, England.
   Bosse, Yohan; Joubert, Philippe, Univ Laval, Inst Univ Cardiol \& Pneumol Quebec, Laval, PQ, Canada.
   Hao, Ke, Icahn Sch Med Mt Sinai, Dept Genet \& Genom Sci, Icahn Inst Data Sci \& Genom Technol, New York, NY 10029 USA.
   Ouwehand, Willem Hendrik, Univ Cambridge, Dept Haematol, Cambridge Biomed Campus, Cambridge, England.
   NHS Blood \& Transplant, Biomed Campus, Cambridge, England.
   Wellcome Sanger Inst, Cambridge, England.
   Roberts, David J., NHS Blood \& Transplant Oxford Ctr, John Radcliffe Hosp, Level 2, Oxford, England.
   Roberts, David J., Univ Oxford, John Radcliffe Hosp, Radcliffe Dept Med, Oxford, England.
   Timens, Wim, Univ Groningen, Dept Pathol \& Med Biol, Groningen, Netherlands.
   van den Berge, Maarten, Univ Groningen, Groningen Res Inst Asthma, Groningen, Netherlands.
   van den Berge, Maarten, Univ Groningen, COPD, Groningen, Netherlands.
   van den Berge, Maarten, Univ Groningen, Dept Pulmonol, Groningen, Netherlands.
   van den Berge, Maarten, Univ Groningen, Groningen Res Inst Asthma, Groningen, Netherlands.
   van den Berge, Maarten, Univ Groningen, COPD, Groningen, Netherlands.
   Butterworth, Adam S.; Danesh, John; Di Angelantonio, Emanuele; Peters, James E., Wellcome Genome Campus, Hlth Data Res UK Cambridge, Cambridge, England.
   Butterworth, Adam S.; Danesh, John; Di Angelantonio, Emanuele; Peters, James E., Univ Cambridge, Cambridge, England.
   Engelhardt, Barbara E., Princeton Univ, Comp Sci Dept, Princeton, NJ 08544 USA.
   Engelhardt, Barbara E., Princeton Univ, Ctr Stat \& Machine Learning, Princeton, NJ 08544 USA.
   Peters, James E., Imperial Coll London, Dept Immunol \& Inflammat, Fac Med, London, England.
   Lunt, Alan C., Cambridge Inst Publ Hlth, MRC Biostat Unit, Robinson Way, Cambridge CB2 0SR, England.},
DOI = {10.1098/rsos.200958},
Article-Number = {200958},
ISSN = {2054-5703},
Keywords = {COVID-19; Mendelian randomization; angiotensin-converting enzyme
   inhibitors; genetic epidemiology},
Keywords-Plus = {RENIN-ANGIOTENSIN SYSTEM; CONVERTING ENZYME 2; HYPERTENSIVE PATIENTS;
   SARS CORONAVIRUS; HEART-FAILURE; RECEPTOR; MODULATION; CARDIOMYOPATHY;
   OLMESARTAN; OUTCOMES},
Research-Areas = {Science \& Technology - Other Topics},
Web-of-Science-Categories  = {Multidisciplinary Sciences},
Author-Email = {sb452@medschl.cam.ac.uk},
Affiliations = {Imperial College London; Johns Hopkins University; Johns Hopkins
   University; Johns Hopkins University; Johns Hopkins University;
   University of Cambridge; University of Cambridge; UK Research \&
   Innovation (UKRI); Medical Research Council UK (MRC); University of
   Cambridge; University of Cambridge; UK Research \& Innovation (UKRI);
   Medical Research Council UK (MRC); MRC Biostatistics Unit; University of
   Cambridge; University of Cambridge; University of Cambridge; St. Paul's
   Hospital; University of British Columbia; Karolinska Institutet; Uppsala
   University; University of Cambridge; University of Cambridge; Pfizer;
   University of Bristol; University of Bristol; Laval University; Icahn
   School of Medicine at Mount Sinai; University of Cambridge; Wellcome
   Trust Sanger Institute; University of Oxford; University of Oxford;
   University of Groningen; University of Groningen; University of
   Groningen; University of Groningen; University of Groningen; University
   of Groningen; University of Cambridge; Princeton University; Princeton
   University; Imperial College London; University of Cambridge; MRC
   Biostatistics Unit},
ResearcherID-Numbers = {Larsson, Susanna C./F-6065-2015
   Timens, Wim/K-5570-2013
   Butterworth, Adam/JOZ-2470-2023
   Sin, Don/AAC-2219-2021
   },
ORCID-Numbers = {Larsson, Susanna C./0000-0003-0118-0341
   Timens, Wim/0000-0002-4146-6363
   Zuber, Verena/0000-0001-9827-1877
   Joubert, Philippe/0000-0001-7784-6387
   Engelhardt, Barbara/0000-0002-6139-7334
   Gill, Dipender/0000-0001-7312-7078
   Karhunen, Ville/0000-0001-6064-1588
   Li, Xuan/0009-0004-1337-3049
   Fahle, Sarah/0000-0002-4359-9952
   van den Berge, Maarten/0000-0002-9336-7340},
Funding-Acknowledgement = {British Heart FoundationCentre of Research Excellence {[}203928/Z/16/Z];
   Wellcome Trust {[}RE/18/4/34215]; Royal Society {[}204623/Z/16/Z]; NIHR
   Blood and Transplant Research Unit in Donor Health and Genomics; UK
   Medical Research Council {[}NIHR BTRU-2014-10024]; British Heart
   Foundation; NIHR (Cambridge Biomedical Research Centre at the Cambridge
   University Hospitals NHS Foundation Trust), and Health Data Research UK
   - NIHR Blood and Transplant Research Unit in Donor Health and Genomics
   {[}SP/09/002, RG/13/13/30194, RG/18/13/33946]; British Heart Foundation
   Professorship {[}NIHR BTRU-2014-10024]; National Institute for Health
   Research Senior Investigator Award - Swedish Heart-Lung Foundation;
   Swedish Research Council; Swedish Research Council for Health, Working
   Life and Welfare - European Union's Horizon 2020 research and innovation
   programme under the Marie Sklodowska-Curie grant {[}721567]; Cancer
   Research UK (CRUK) Integrative Cancer Epidemiology Programme; Academic
   Clinical Fellowship from the NIHR {[}C18281/A19169]; Canada Research
   Chair in Genomics of Heart and Lung Diseases; UKRI Innovation Fellowship
   at Health Data Research UK {[}MR/S004068/1]; National Institute for
   Health Research {[}Cambridge Biomedical Research Centre at the Cambridge
   University Hospitals NHS Foundation Trust] - European Council Innovative
   Medicines Initiative (BigData@Heart); Health Data Research UK - UK
   Medical Research Council, Engineering and Physical Sciences Research
   Council; Economic and Social Research Council, Department of Health and
   Social Care (England), Chief Scientist Office of the Scottish Government
   Health and Social Care Directorates, Health and Social Care Research and
   Development Division (Welsh Government); Public Health Agency (Northern
   Ireland); Wellcome Trust - National Institute for Health Research
   (NIHR); NIHR (Cambridge Biomedical Research Centre at the Cambridge
   University Hospitals NHS Foundation Trust) - Leidos Biomedical, Inc.
   (Leidos) {[}10XS170]; Roswell Park Cancer Institute; Leidos {[}10XS171,
   HHSN268201000029C, 10ST1035];  {[}HHSN261200800001E]; MRC
   {[}MR/S004068/2] Funding Source: UKRI},
Funding-Text = {D.G. is supported by theWellcome Trust 4i Programme (203928/Z/16/Z) and
   British Heart FoundationCentre of Research Excellence (RE/18/4/34215) at
   Imperial College London. S.B. is supported by a Sir Henry Dale
   Fellowship jointly funded by the Wellcome Trust and the Royal Society
   (award no. 204623/Z/16/Z). The academic coordinating centre for INTERVAL
   at Cambridge University was supported by core funding from: NIHR Blood
   and Transplant Research Unit in Donor Health and Genomics (NIHR
   BTRU-2014-10024), UK Medical Research Council (MR/L003120/1), British
   Heart Foundation (SP/09/002; RG/13/13/30194; RG/18/13/33946) and the
   NIHR (Cambridge Biomedical Research Centre at the Cambridge University
   Hospitals NHS Foundation Trust), and Health Data Research UK. S.F. is
   funded by the NIHR Blood and Transplant Research Unit in Donor Health
   and Genomics (NIHR BTRU-2014-10024). J.D. holds a British Heart
   Foundation Professorship and a National Institute for Health Research
   Senior Investigator Award. S.C.L. is funded by the Swedish Heart-Lung
   Foundation, the Swedish Research Council and the Swedish Research
   Council for Health, Working Life and Welfare. V.K. is funded by a
   European Union's Horizon 2020 research and innovation programme under
   the Marie Sklodowska-Curie grant no. 721567. V.Y.T. is supported by the
   Cancer Research UK (CRUK) Integrative Cancer Epidemiology Programme
   (C18281/A19169). S.M.L. is supported by an Academic Clinical Fellowship
   from the NIHR. Y.B. holds a Canada Research Chair in Genomics of Heart
   and Lung Diseases. J.E.P. is supported by a UKRI Innovation Fellowship
   at Health Data Research UK (MR/S004068/1). T.J. is funded by the
   National Institute for Health Research {[}Cambridge Biomedical Research
   Centre at the Cambridge University Hospitals NHS Foundation Trust].
   A.M.M. is funded by the European Council Innovative Medicines Initiative
   (BigData@Heart).This work was supported by Health Data Research UK,
   which is funded by the UK Medical Research Council, Engineering and
   Physical Sciences Research Council, Economic and Social Research
   Council, Department of Health and Social Care (England), Chief Scientist
   Office of the Scottish Government Health and Social Care Directorates,
   Health and Social Care Research and Development Division (Welsh
   Government), Public Health Agency (Northern Ireland), British Heart
   Foundation and the Wellcome Trust. DNA extraction and genotyping was
   co-funded by the National Institute for Health Research (NIHR), the NIHR
   BioResource (http://bioresource.nihr.ac.uk) and the NIHR (Cambridge
   Biomedical Research Centre at the Cambridge University Hospitals NHS
   Foundation Trust). Donors were enrolled at Biospecimen Source Sites
   funded by Leidos Biomedical, Inc. (Leidos) subcontracts to the National
   Disease Research Interchange (10XS170) and Roswell Park Cancer Institute
   (10XS171). The Laboratory, Data Analysis and Coordinating Center (LDACC)
   was funded through a contract (HHSN268201000029C) to The Broad
   Institute, Inc. Biorepository operations were funded through a Leidos
   subcontract to Van Andel Institute (10ST1035). Additional data
   repository and project management provided by Leidos
   (HHSN261200800001E).},
Number-of-Cited-References = {73},
Times-Cited = {8},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {R. Soc. Open Sci.},
Doc-Delivery-Number = {PA2LW},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000595466300001},
OA = {Green Published, gold, Green Submitted, Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000956648600001,
Author = {LaBrie, Richard and Hupfer, Michael and Lau, Maximilian P.},
Title = {Anaerobic duration predicts biogeochemical consequences of oxygen
   depletion in lakes},
Journal = {LIMNOLOGY AND OCEANOGRAPHY LETTERS},
Year = {2023},
Volume = {8},
Number = {4},
Pages = {666-674},
Month = {AUG},
Abstract = {Lake deoxygenation is of growing concern because it threatens ecosystem
   services delivery. Complete deoxygenation, anoxia, is projected to
   prolong and expand in lakes, promoting the production or release of
   nutrients, greenhouse gases and metals from the water column and
   sediments. Accumulation of these compounds cannot be easily predicted
   thus hindering our capacity to forecast the ecological consequences of
   global changes on aquatic ecosystems. Here, we used monitoring data of
   four lakes to develop a novel tool, anaerobic duration, to study
   anaerobic processes in lake waters. Anaerobic duration explained, as a
   single predictor, 21-60\% of the variation for ammonium, phosphorus and
   a dissolved organic matter fluorophore. Anaerobic duration could be
   modeled using only two oxygen profiles and lake bathymetry, making it an
   easily applicable tool to interpret and extrapolate biogeochemical data.
   This novel tool thus has the potential to transform widely available
   oxygen profiles into an ecologically meaningful variable.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Lau, MP (Corresponding Author), TU Bergakademie Freiberg, Interdisciplinary Environm Res Ctr, Freiberg, Germany.
   Lau, MP (Corresponding Author), Leibniz Inst Freshwater Ecol \& Inland Fisheries IG, Berlin, Germany.
   LaBrie, Richard; Lau, Maximilian P., TU Bergakademie Freiberg, Interdisciplinary Environm Res Ctr, Freiberg, Germany.
   Hupfer, Michael; Lau, Maximilian P., Leibniz Inst Freshwater Ecol \& Inland Fisheries IG, Berlin, Germany.
   Hupfer, Michael, Brandenburg Tech Univ Cottbus Senftenberg, Dept Aquat Ecol, Bad Saarow Pieskow, Germany.},
DOI = {10.1002/lol2.10324},
EarlyAccessDate = {MAR 2023},
EISSN = {2378-2242},
Keywords-Plus = {DISSOLVED ORGANIC-MATTER; TEMPERATE; ANOXIA; RATES; CONSUMPTION;
   DYNAMICS; MINIMUM; RELEASE; MARINE},
Research-Areas = {Marine \& Freshwater Biology; Oceanography},
Web-of-Science-Categories  = {Limnology; Marine \& Freshwater Biology; Oceanography},
Author-Email = {maximilian.lau@ioez.tu-freiberg.de},
Affiliations = {Technical University Freiberg; Leibniz Institut fur Gewasserokologie und
   Binnenfischerei (IGB); Brandenburg University of Technology Cottbus},
ResearcherID-Numbers = {LaBrie, Richard/D-6386-2018},
ORCID-Numbers = {LaBrie, Richard/0000-0003-1681-4888},
Funding-Acknowledgement = {State Agency for Flood Protection and Water Management Saxony-Anhalt;
   Projekt DEAL},
Funding-Text = {We would like to thank Sylvia Jordan (IGB) for managing the long-term
   program in Arendsee and for her help with data validation, and Sabine
   Wollrab for handling the data repository process. We are grateful to
   Christiane Herzog and Thomas Rossoll (IGB) for laboratory work and other
   technical support. We acknowledge Tobias Goldhammer (IGB) for
   discussions and for the support as head of the Chemical Laboratory. We
   would like to thank Thomas Shatwell (Helmholtz-Zentrum fur
   Umweltforschung) for insightful discussions, and two independent
   reviewers for constructive criticisms. The monitoring program is partly
   supported by the State Agency for Flood Protection and Water Management
   Saxony-Anhalt (LHW). We acknowledge the long-term monitoring program of
   Lake Stechlin by the Department of Plankton and Microbial Ecology of the
   Leibniz Institute of Freshwater Ecology and Inland Fisheries (IGB),
   Germany. Open Access funding enabled and organized by Projekt DEAL.},
Number-of-Cited-References = {41},
Times-Cited = {1},
Usage-Count-Last-180-days = {3},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Limnol. Oceanogr. Lett.},
Doc-Delivery-Number = {L8HN9},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000956648600001},
OA = {gold},
DA = {2024-01-15},
}

@article{ WOS:000576191500010,
Author = {Denamiel, Clea and Huan, Xun and Sepic, Jadranka and Vilibic, Ivica},
Title = {Uncertainty Propagation Using Polynomial Chaos Expansions for Extreme
   Sea Level Hazard Assessment: The Case of the Eastern Adriatic
   Meteotsunamis},
Journal = {JOURNAL OF PHYSICAL OCEANOGRAPHY},
Year = {2020},
Volume = {50},
Number = {4},
Pages = {1005-1021},
Month = {APR},
Abstract = {This study quantifies the hazard associated with extreme sea levels due
   to eastern Adriatic meteotsunamis-long waves generated by traveling
   atmospheric disturbances-and assesses the sensitivity of the ocean
   response to the disturbances responsible for those events. In this
   spirit, a surrogate model of meteotsunami maximum elevation based on
   generalized polynomial chaos expansion (gPCE) methods, is implemented.
   The approach relies on the definition of a synthetic pressure
   disturbance-depending on six different stochastic parameters known to be
   important for meteotsunami generation, which is used as forcing to
   produce series of meteotsunami simulations defined with sparse grid
   methods (up to 10 689 used in this study). The surrogate model and the
   sensitivity study are then obtained with a pseudo-spectral approximation
   (PSA) method based on the chosen meteotsunami simulations. This study
   mainly presents the developed methodology and discusses the feasibility
   of implementing such gPCE-based surrogate models to assess the hazard
   and to study the sensitivity of meteorologically driven extreme sea
   levels.},
Publisher = {AMER METEOROLOGICAL SOC},
Address = {45 BEACON ST, BOSTON, MA 02108-3693 USA},
Type = {Article},
Language = {English},
Affiliation = {Denamiel, C (Corresponding Author), Inst Oceanog \& Fisheries, Split, Croatia.
   Denamiel, Clea; Sepic, Jadranka; Vilibic, Ivica, Inst Oceanog \& Fisheries, Split, Croatia.
   Huan, Xun, Univ Michigan, Ann Arbor, MI 48109 USA.},
DOI = {10.1175/JPO-D-19-0147.1},
ISSN = {0022-3670},
EISSN = {1520-0485},
Keywords = {Atmosphere-ocean interaction; Probability forecasts; models;
   distribution; Ocean models; Stochastic models; Flood events; Risk
   assessment},
Keywords-Plus = {GLOBAL SENSITIVITY-ANALYSIS; STOCHASTIC FINITE-ELEMENTS; MODELING
   UNCERTAINTY; BAYESIAN-INFERENCE; OCEAN WAVES; BUOY DATA; FLOW;
   QUADRATURE; JUNE; QUANTIFICATION},
Research-Areas = {Oceanography},
Web-of-Science-Categories  = {Oceanography},
Author-Email = {cdenamie@izor.hr},
Affiliations = {Croatian Institute of Oceanography \& Fisheries (IZOR); University of
   Michigan System; University of Michigan},
ResearcherID-Numbers = {Denamiel, Clea Lumina/AAY-3909-2021
   Huan, Xun/A-3025-2017
   Sepic, Jadranka/HPF-2045-2023
   Vilibic, Ivica/AAE-5160-2019},
ORCID-Numbers = {Denamiel, Clea Lumina/0000-0002-5099-1143
   Huan, Xun/0000-0001-6544-2764
   Sepic, Jadranka/0000-0002-5624-1351
   },
Funding-Acknowledgement = {project MESSI (UKF Grant) {[}25/15]; project ADIOS (Croatian Science
   Foundation Grant) {[}IP-201606-1955]; ECMWF Special Project (The
   Adriatic decadal and inter-annual oscillations: modelling component)},
Funding-Text = {Acknowledgement is made for the support of the ECMWF staff, in
   particular Xavier Abellan, as well as for ECMWF's computing and archive
   facilities used in this research, which has been supported by projects
   MESSI (UKF Grant 25/15), ADIOS (Croatian Science Foundation Grant
   IP-201606-1955), and ECMWF Special Project (The Adriatic decadal and
   inter-annual oscillations: modelling component). The authors would also
   like to thank the anonymous reviewers for their valuable contributions.
   The data and MATLAB programs used to create the gPCE-based meteotsunami
   surrogate model, as well as the sensitivity study, can be obtained under
   the Open Science Framework (OSF) FAIR data repository at
   https://osf.io/jysqu/(doi:10.17605/OSF.IO/JYSQU).},
Number-of-Cited-References = {80},
Times-Cited = {12},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Phys. Oceanogr.},
Doc-Delivery-Number = {NY1XQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000576191500010},
DA = {2024-01-15},
}

@article{ WOS:000519719500013,
Author = {Kyburz, M. L. and Sovilla, Betty and Gaume, Johan and Ancey, Christophe},
Title = {Decoupling the Role of Inertia, Friction, and Cohesion in Dense Granular
   Avalanche Pressure Build-up on Obstacles},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE},
Year = {2020},
Volume = {125},
Number = {2},
Month = {FEB},
Abstract = {Understanding the physical processes involved in snow avalanche-obstacle
   interaction is essential to be able to estimate the pressure exerted on
   structures. Although avalanche impact pressure has been measured in
   field experiments for decades, the underlying physical principles are
   still elusive. Previous studies suggest that pressure is increased due
   to the formation of an influenced flow region around the structure, the
   mobilized domain, which varies in size depending on snow properties such
   as snow cohesion. Here, we aim to better understand how cohesion,
   friction, velocity, and their interplay affect avalanche pressure
   buildup on structures. This is achieved by simulating the
   avalanche-obstacle interaction with a newly developed numerical model
   based on the discrete element method, using a cohesive bond contact law.
   The relevance of the model is tested by comparing simulated impact
   pressures with field measurements from the Vallee de la Sionne
   experimental site. Our results show that at the macroscale, impact
   pressure consists of the inertial, frictional, and cohesive
   contributions. The inertial and frictional contributions arise due to
   the existence, shape, and dimension of the mobilized domain. The
   cohesive contribution increases the particle contact forces inside the
   domain, leading up to a doubling of the pressure. Based on these
   physical processes, we propose a novel scaling law to reduce the problem
   of calculating the pressure induced by cohesive flows, to the
   calculation of cohesionless flows. These findings enhance our
   understanding of the interaction of cohesive granular flows, such as
   snow avalanches, and structures at the microscale and macroscale.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Kyburz, ML (Corresponding Author), WSL Inst Snow \& Avalanche Res SLF, Davos, Switzerland.
   Kyburz, ML (Corresponding Author), Swiss Fed Inst Technol, Environm Hydraul Lab, Lausanne, Switzerland.
   Kyburz, M. L.; Sovilla, Betty; Gaume, Johan, WSL Inst Snow \& Avalanche Res SLF, Davos, Switzerland.
   Kyburz, M. L.; Ancey, Christophe, Swiss Fed Inst Technol, Environm Hydraul Lab, Lausanne, Switzerland.
   Gaume, Johan, Swiss Fed Inst Technol, Snow \& Avalanche Simulat Lab SLAB, Lausanne, Switzerland.},
DOI = {10.1029/2019JF005192},
Article-Number = {e2019JF005192},
ISSN = {2169-9003},
EISSN = {2169-9011},
Keywords = {cohesive granular flow; impact pressure on structure; snow avalanche;
   discrete element method},
Keywords-Plus = {TEST-SITE; IMPACT PRESSURE; FLOW REGIME; SLOW DRAG; SNOW; FORCE; MODEL},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {kyburz@slf.ch},
Affiliations = {Swiss Federal Institutes of Technology Domain; Swiss Federal Institute
   for Forest, Snow \& Landscape Research; Swiss Federal Institutes of
   Technology Domain; Ecole Polytechnique Federale de Lausanne; Swiss
   Federal Institutes of Technology Domain; Ecole Polytechnique Federale de
   Lausanne},
ORCID-Numbers = {Ancey, Christophe/0000-0003-3354-7398
   Kyburz, Michael/0000-0002-2929-7771
   Sovilla, Betty/0000-0001-8771-6439
   Gaume, Johan/0000-0001-8931-752X},
Funding-Acknowledgement = {Swiss National Science Foundation {[}200021\_169640, PCEFP2\_181227];
   Horizon 2020 project OpenAIRE; Swiss National Science Foundation (SNF)
   {[}200021\_169640, PCEFP2\_181227] Funding Source: Swiss National
   Science Foundation (SNF)},
Funding-Text = {Michael Kyburz, Betty Sovilla, and Christophe Ancey acknowledge the
   Swiss National Science Foundation for funding this project ``Pressure on
   obstacles induced by granular snow avalanches{''} (Grant
   200021\_169640). Johan Gaume acknowledges financial support from the
   Swiss National Science Foundation (Grant PCEFP2\_181227). The supporting
   information and the code to be used with the Itasca PFC3D software to
   reproduce the data presented in this paper are available in the open
   access data repository Zenodo, which is financed by the Horizon 2020
   project OpenAIRE and hosted by CERN. The associated entry can be
   accessed via Kyburz M. L., Sovilla, B., Gaume J., and Ancey C. (2019).
   Decoupling the role of inertia, friction, and cohesion in dense granular
   avalanche pressure buildup on obstacles {[}Supporting Information].
   Zenodo (https://doi.org/10.5281/zenodo.3239031).We would like to thank
   the Editor Ton Hoitink, the Associate Editor Michele Bolla Pittaluga, as
   well as Thierry Faug and two anonymous reviewers for their helpful
   comments.},
Number-of-Cited-References = {59},
Times-Cited = {9},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {16},
Journal-ISO = {J. Geophys. Res.-Earth Surf.},
Doc-Delivery-Number = {KU4ZM},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000519719500013},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000407627100026,
Author = {Nishi, Katsuki and Shiokawa, Kazuo and Fruehauff, Dennis},
Title = {Conjugate observation of auroral finger-like structures by ground-based
   all-sky cameras and THEMIS satellites},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2017},
Volume = {122},
Number = {7},
Pages = {7291-7306},
Month = {JUL},
Abstract = {In this study, we analyze the first conjugate observation of auroral
   finger-like structures using ground-based all-sky cameras and the Time
   History of Events and Macroscale Interactions during Substorms (THEMIS)
   satellites and investigated associated physical processes that are a
   cause of auroral fragmentation into patches. Two events are reported:
   one is a conjugate event, and the other is a nearly conjugate event. The
   conjugate event was observed at Narsarsuaq (magnetic latitude: 65.3
   degrees N), Greenland, at 0720-0820 UT (0506-0606 LT) on 17 February
   2012. Analysis of the event revealed the following observational facts:
   (1) variation of parallel electron energy fluxes observed by THEMIS-E
   shows a correspondence to the auroral intensity variation, (2) plasma
   pressure and magnetic pressure fluctuate in antiphase with time scales
   of 5-20 min, and (3) perpendicular ion velocity is very small (less than
   50 km/s). In the latter event, observed at Gakona, Alaska, on 2 February
   2008, the THEMIS-D satellite passed across higher latitudes of
   finger-like structures. The data from THEMIS-D also showed the antiphase
   fluctuation between plasma pressure and magnetic pressure and the small
   perpendicular ion velocity. From these observations, we suggest that the
   finger-like structures are caused by a pressure-driven instability in
   the balance of plasma and magnetic pressures in the magnetosphere.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Nishi, K (Corresponding Author), Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan.
   Nishi, Katsuki; Shiokawa, Kazuo, Nagoya Univ, Inst Space Earth Environm Res, Nagoya, Aichi, Japan.
   Fruehauff, Dennis, Tech Univ Carolo Wilhelmina Braunschweig, Inst Geophys \& Extraterr Phys, Braunschweig, Germany.},
DOI = {10.1002/2016JA023774},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords-Plus = {PLASMA SHEET; PATCHES; FRAGMENTATION; MAGNETOSPHERE; INSTRUMENT; PHYSICS},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {k-nishi@isee.nagoya-u.ac.jp},
Affiliations = {Nagoya University; Braunschweig University of Technology},
ORCID-Numbers = {Nishi, Katsuki/0000-0003-4863-649X},
Funding-Acknowledgement = {NASA {[}NAS5-02099]; German Ministry for Economy and Technology; German
   Center for Aviation and Space (DLR) {[}50 OC 0302]; NSF {[}AGS-1004736,
   AGS-1004814]; KAKENHI grant by the Japan Society for the Promotion of
   Science {[}15H05815, 16H06286]; Directorate For Geosciences {[}1004736]
   Funding Source: National Science Foundation; Div Atmospheric \& Geospace
   Sciences {[}1004736] Funding Source: National Science Foundation},
Funding-Text = {The Conjunction Event Finder at DARTS JAXA/ISAS provided useful
   information for this study. We acknowledge NASA contract NAS5-02099 and
   V. Angelopoulos for the use of data from the THEMIS mission.
   Specifically, we thank C.W. Carlson and J.P. Mcfadden for use of ESA
   data; J.W. Bonnell and F.S. Mozer for use of EFI data; D. Larson for use
   of SST data; K.H. Glassmeier, U. Auster, and W. Baumjohann for the use
   of FGM data provided under the lead of the Technical University of
   Braunschweig and with financial support through the German Ministry for
   Economy and Technology and the German Center for Aviation and Space
   (DLR) under contract 50 OC 0302; S. Mende and E. Donovan for use the ASI
   data, the CSA for logistical support in fielding and data retrieval from
   the GBO stations, and NSF for support of GIMNAST through grant
   AGS-1004736; S. Mende and C.T. Russell for use of the GMAG data and NSF
   for support through grant AGS-1004814; and I.R. Mann, D.K. Milling, and
   the rest of the CARISMA team for use of GMAG data. CARISMA is operated
   by the University of Alberta, funded by the Canadian Space Agency. Data
   provided by the Geophysical Institute Magnetometer Array operated by the
   Geophysical Institute, University of Alaska. More information about this
   data set is available at http://magnet.asf.alaska.edu/, and magnetometer
   data from the Greenland Magnetometer Array were provided by the National
   Space Institute at the Technical University of Denmark. THEMIS probes,
   geomagnetic field, and all-sky image data are available through the open
   data repository at UC Berkeley at
   http://themis.ssl.berkeley.edu/index.shtml. The T96 model was obtained
   from the GSFC/SPDF OMNIWeb interface at http://omniweb. gsfc.nasa.gov.
   This work was supported by KAKENHI grants 15H05815 and 16H06286 provided
   by the Japan Society for the Promotion of Science.},
Number-of-Cited-References = {39},
Times-Cited = {4},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {FD6GN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000407627100026},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000588710900001,
Author = {Baumer, Marlene M. and Wagner, Bernd and Meyer, Hanno and Leicher,
   Niklas and Lenz, Matthias and Fedorov, Grigory and Pestryakova, Luidmila
   A. and Melles, Martin},
Title = {Climatic and environmental changes in the Yana Highlands of
   north-eastern Siberia over the last <i>c</i>. 57 000 years, derived from
   a sediment core from Lake Emanda},
Journal = {BOREAS},
Year = {2021},
Volume = {50},
Number = {1},
Pages = {114-133},
Month = {JAN},
Abstract = {The sediment succession of Lake Emanda in the Yana Highlands was
   investigated to reconstruct the regional late Quaternary climate and
   environmental history. Hydro-acoustic data obtained during a field
   campaign in 2017 show laminated sediments in the north-western and
   deepest (up to -m) part of the lake, where a similar to 6-m-long
   sediment core (Co1412) was retrieved. The sediment core was studied with
   a multi-proxy approach including sedimentological and geochemical
   analyses. The chronology of Co1412 is based on C-14 AMS dating on plant
   fragments from the upper 4.65 m and by extrapolation suggests a basal
   age of c. 57 cal. ka BP. Pronounced changes in the proxy data indicate
   that early Marine Isotope Stage (MIS) 3 was characterized by unstable
   environmental conditions associated with short-term temperature and/or
   precipitation variations. This interval was followed by progressively
   colder and likely drier conditions during mid-MIS 3. A lake-level
   decline between 32.0 and 19.1 cal. ka BP was presumably related to
   increased continentality and dry conditions peaking during the Last
   Glacial Maximum (LGM). A subsequent rise in lake level could accordingly
   have been the result of increased rainfall, probably in combination with
   seasonally high meltwater input. A milder or wetter Lateglacial climate
   increased lake productivity and vegetation growth, the latter
   stabilizing the catchment and reducing clastic input into the lake. The
   Bolling-Allerod warming, Younger Dryas cooling and Holocene Thermal
   Maximum (HTM) are indicated by distinct changes in the environment
   around Lake Emanda. Unstable, but similar-to-present-day climatic and
   environmental conditions have persisted since c. 5 cal. ka BP. The
   results emphasize the highly continental setting of the study site and
   therefore suggest that the climate at Lake Emanda was predominantly
   controlled by changes in summer insolation, global sea level, and the
   extent of ice sheets over Eurasia, which influenced atmospheric
   circulation patterns.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Baumer, MM (Corresponding Author), Univ Cologne, Inst Geol \& Mineral, Zulpicher Str 49a, D-50674 Cologne, Germany.
   Baumer, Marlene M.; Wagner, Bernd; Leicher, Niklas; Lenz, Matthias; Melles, Martin, Univ Cologne, Inst Geol \& Mineral, Zulpicher Str 49a, D-50674 Cologne, Germany.
   Meyer, Hanno, Res Dept Potsdam, Helmholtz Ctr Polar \& Marine Res, Alfred Wegener Inst, Dept Periglacial Res, Telegrafenberg A43, D-14473 Potsdam, Germany.
   Fedorov, Grigory, St Petersburg State Univ, Inst Earth Sci, Geomorphol Dept, Univ Skaya Nab 7-9, St Petersburg 199034, Russia.
   Fedorov, Grigory, Arctic \& Antarctic Res Inst, Dept Geog Polar Reg, Bering Str 38, St Petersburg 199397, Russia.
   Pestryakova, Luidmila A., North Eastern Fed Univ Yakutsk, Inst Biochem \& Biol, Belinsky St 58, Yakutsk 677000, Russia.},
DOI = {10.1111/bor.12476},
EarlyAccessDate = {NOV 2020},
ISSN = {0300-9483},
EISSN = {1502-3885},
Keywords-Plus = {LATE QUATERNARY GLACIATIONS; POLAR URAL MOUNTAINS; LENA RIVER DELTA;
   SEA-LEVEL CHANGE; VERKHOYANSK MOUNTAINS; ORGANIC-MATTER; POLLEN RECORD;
   HOLOCENE TRANSITION; VEGETATION HISTORY; ICE COMPLEX},
Research-Areas = {Physical Geography; Geology},
Web-of-Science-Categories  = {Geography, Physical; Geosciences, Multidisciplinary},
Author-Email = {baumermarlene@googlemail.com},
Affiliations = {University of Cologne; Helmholtz Association; Alfred Wegener Institute,
   Helmholtz Centre for Polar \& Marine Research; Saint Petersburg State
   University; Arctic \& Antarctic Research Institute; North-Eastern
   Federal University in Yakutsk},
ResearcherID-Numbers = {Meyer, Hanno/AAQ-4260-2021
   Pestryakova, Luidmila/Q-9900-2016
   Melles, Martin/J-4070-2012
   Wagner, Bernd/J-4682-2012
   Fedorov, Grigory/N-5788-2019
   },
ORCID-Numbers = {Meyer, Hanno/0000-0003-4129-4706
   Pestryakova, Luidmila/0000-0001-5347-4478
   Melles, Martin/0000-0003-0977-9463
   Wagner, Bernd/0000-0002-1369-7893
   Fedorov, Grigory/0000-0003-2269-4501
   Leicher, Niklas/0000-0002-3367-5982
   Lenz (nee Baumer), Marlene Margit/0000-0002-5352-3900},
Funding-Acknowledgement = {German Federal Ministry of Education and Research (BMBF) {[}03F0830A];
   Russian Foundation for Basic Research {[}18-45-140053 r\_a]; Russian
   Ministry of Education and Science {[}FSRG-2020-0019]; Projekt DEAL},
Funding-Text = {Financial support for this study was provided by the German Federal
   Ministry of Education and Research (BMBF; grant no. 03F0830A). The work
   of L. Pestryakova was sponsored by the Russian Foundation for Basic
   Research (grant no. 18-45-140053 r\_a) and the Russian Ministry of
   Education and Science (FSRG-2020-0019). We are grateful to various
   colleagues from the North-Eastern Federal University in Yakutsk for
   their logistical help during the fieldwork in summer 2017. We also
   acknowledge Dima Bolshiyanov from the Arctic and Antarctic Research
   Institute in St. Petersburg for his participation in the field campaign.
   Nicole Mantke and Dorothea Klinghardt from the University of Cologne are
   acknowledged for their assistance during laboratory work. We also thank
   P. Tarasov and another anonymous reviewer as well as the editor Jan A.
   Piotrowski for their constructive comments. Proxy data of core Co1412
   are available via the PANGAEA data repository after publication. The
   authors have no conflict of interest, financial or otherwise, to
   declare. Open access funding enabled and organized by Projekt DEAL.},
Number-of-Cited-References = {118},
Times-Cited = {10},
Usage-Count-Last-180-days = {4},
Usage-Count-Since-2013 = {13},
Journal-ISO = {Boreas},
Doc-Delivery-Number = {PT4EY},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000588710900001},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000534472900002,
Author = {Powell, Elisabeth B. and Krause, Johannes R. and Martin, Rose M. and
   Watson, Elizabeth Burke},
Title = {Pond Excavation Reduces Coastal Wetland Carbon Dioxide Assimilation},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES},
Year = {2020},
Volume = {125},
Number = {2},
Month = {FEB},
Abstract = {Coastal wetlands comprise important global carbon sinks; however,
   anthropogenic disturbance accompanied with accelerating sea level rise
   threaten their continued survival. In this study, we quantified habitat
   disturbance to salt marshes in Barnegat Bay, New Jersey, resulting from
   the construction of ponds for mosquito control. Geographic object-based
   image analysis of high-resolution four-band aerial imagery revealed that
   over 7,000 ponds were constructed in the marsh complex with pond
   densities as high as 290 ponds per km(2). Physical disturbance from pond
   creation and sediment dispersal extended to over 17\% of the bay's tidal
   wetlands. By tracking recolonization of vegetation, we estimated that it
   took 5 years for 51\% vegetation recovery and 10 years for 69\%
   recovery, with complete recover (100\%) not expected for more than 50
   years. This suggests that efforts to extend the lifespan of drowning
   coastal wetlands through sediment additions might disrupt carbon dioxide
   assimilation, as effects of disturbance persist. Focusing on greenhouse
   gas exchange, our work found that areas of marsh vegetation contribute
   to carbon assimilation (-42 g C . m(-2) . year(-1)), while ponds and
   areas of bare peat created by pond excavation were associated with
   carbon emissions (44 and 125 g C . m(-2) . year(-1), respectively).
   These results suggest that the conversion of wetlands to ponds-which is
   a significant driver of coastal wetland loss worldwide-may convert
   coastal wetlands from greenhouse gas sinks to sources. Additionally,
   quantifying the area of vegetation within a marsh (vs. bare ground or
   open water) is important for quantifying their greenhouse gas mitigation
   function.
   Plain Language Summary Coastal wetlands are important for our planet as
   they remove carbon dioxide from the atmosphere. Our goal was to
   determine how the construction of ponds in wetlands-which is common
   worldwide to support expanding aquaculture-affects the ability of
   marshes to take up carbon dioxide. We estimated the number and extent of
   ponds constructed for mosquito control in coastal wetlands in Barnegat
   Bay, New Jersey. Additionally, we measured greenhouse gas exchange from
   the ponds, surrounding intact marsh, and in bare areas at several sites
   across the growing season to estimate the total carbon uptake of the
   whole marsh. We found that over 7,000 ponds have been dug for mosquito
   control in New Jersey and that pond density is as high as 290 ponds per
   km(2). We also found that the ponds constructed in wetlands reduce the
   ability of wetlands to remove carbon dioxide from the atmosphere.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Powell, EB (Corresponding Author), Drexel Univ, Acad Nat Sci, Dept Biodivers Earth \& Environm Sci, Philadelphia, PA 19104 USA.
   Powell, Elisabeth B.; Krause, Johannes R.; Watson, Elizabeth Burke, Drexel Univ, Acad Nat Sci, Dept Biodivers Earth \& Environm Sci, Philadelphia, PA 19104 USA.
   Martin, Rose M., US EPA, Atlantic Ecol Div, ORD NHEERL, Narragansett, RI USA.
   Martin, Rose M., Dataquest Labs, San Francisco, CA USA.},
DOI = {10.1029/2019JG005187},
ISSN = {2169-8953},
EISSN = {2169-8961},
Keywords = {pond construction; carbon dioxide; methane; mosquito; OMWM; open marsh
   water management},
Keywords-Plus = {MID-ATLANTIC COAST; SALT-MARSH; METHANE EMISSIONS; BLUE CARBON;
   LAND-USE; BAY; VEGETATION; DYNAMICS; POOLS; ACCUMULATION},
Research-Areas = {Environmental Sciences \& Ecology; Geology},
Web-of-Science-Categories  = {Environmental Sciences; Geosciences, Multidisciplinary},
Author-Email = {elisabethpowell35@gmail.com},
Affiliations = {Drexel University; United States Environmental Protection Agency},
ORCID-Numbers = {Krause, Johannes/0000-0001-5721-6353
   Watson, Elizabeth/0000-0002-8496-1647},
Funding-Acknowledgement = {U.S. Environmental Protection Agency {[}CE98212312]; New Jersey Sea
   Grant Consortium (NJSGC); National Oceanic and Atmospheric
   Administration (NOAA) Office of Sea Grant, U.S. Department of Commerce,
   under NOAA {[}NA14OAR4170085]; Garden Club of American; Society of
   Wetland Scientists; Barnegat Bay Partnership; AWIS-PHL; Ocean County
   Natural Lands Trust},
Funding-Text = {This work was supported by the U.S. Environmental Protection Agency,
   under award CE98212312, and the New Jersey Sea Grant Consortium (NJSGC)
   with funds from the National Oceanic and Atmospheric Administration
   (NOAA) Office of Sea Grant, U.S. Department of Commerce, under NOAA
   grant number NA14OAR4170085. The statements, findings, conclusions, and
   recommendations are those of the authors and do not necessarily reflect
   the views of the NJSGC or the U.S. Department of Commerce
   {[}NJSG-19941]. We thank the Garden Club of American, the Society of
   Wetland Scientists, the Barnegat Bay Partnership, AWIS-PHL, and Ocean
   County Natural Lands Trust for supporting this study and the State of
   New Jersey Department of Environmental Protection and the staff of
   Cattus Island County Park for access to research sites. We thank K.
   Raper, L. Champlin, S. Courtney, D. Wolfinger, C. Ibarra, and F. Rahman
   for assistance with fieldwork, T. Elsey-Quirk for biomass data, and D.
   Velinsky, T. Mozdzer, and C. Wigand for constructive feedback. Research
   data are available through the DRYAD open-access data repository
   (https://doi.org/10.5061/dryad.3j9kd51d2).},
Number-of-Cited-References = {73},
Times-Cited = {8},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {43},
Journal-ISO = {J. Geophys. Res.-Biogeosci.},
Doc-Delivery-Number = {LP7BS},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000534472900002},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000499546200001,
Author = {Denamiel, Clea and Sepic, Jadranka and Huan, Xun and Bolzer, Celia and
   Vilibic, Ivica},
Title = {Stochastic Surrogate Model for Meteotsunami Early Warning System in the
   Eastern Adriatic Sea},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS},
Year = {2019},
Volume = {124},
Number = {11},
Pages = {8485-8499},
Month = {NOV},
Abstract = {The meteotsunami early warning system prototype using stochastic
   surrogate approach and running operationally in the eastern Adriatic Sea
   is presented. First, the atmospheric internal gravity waves (IGWs)
   driving the meteotsunamis are either forecasted with state-of-the-art
   deterministic models at least a day in advance or detected through
   measurements at least 2 hr before the meteotsunami reaches sensitive
   locations. The extreme sea-level hazard forecast at endangered locations
   is then derived with an innovative stochastic surrogate
   model-implemented with generalized polynomial chaos expansion (gPCE)
   method and synthetic IGWs forcing a barotropic ocean model-used with the
   input parameters extracted from deterministic model results and/or
   measurements. The evaluation of the system, both against five historical
   events and for all the detected potential meteotsunamis since late 2018
   when the early warning system prototype became operational, reveals that
   the meteotsunami hazard is conservatively assessed but often
   overestimated at some locations. Despite some needed improvements and
   developments, this study demonstrates that gPCE-based methods can be
   used for atmospherically driven extreme sea-level hazard assessment and
   in geosciences in wide.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Denamiel, C (Corresponding Author), Inst Oceanog \& Fisheries, Lab Phys, Split, Croatia.
   Denamiel, Clea; Sepic, Jadranka; Vilibic, Ivica, Inst Oceanog \& Fisheries, Lab Phys, Split, Croatia.
   Huan, Xun, Univ Michigan, Mech Engn, Ann Arbor, MI 48109 USA.
   Bolzer, Celia, Univ Toulon \& Var, Ecole Ingn, SeaTech, Toulon, France.
   Bolzer, Celia, EniProgetti Eni House, Basingstoke, Hants, England.},
DOI = {10.1029/2019JC015574},
EarlyAccessDate = {NOV 2019},
ISSN = {2169-9275},
EISSN = {2169-9291},
Keywords = {meteotsunami early warning system; extreme sea-level hazard assessment;
   eastern Adriatic},
Keywords-Plus = {POLYNOMIAL CHAOS; UNCERTAINTY QUANTIFICATION; SENSITIVITY-ANALYSIS;
   FIELD SURVEY; BUOY DATA; TSUNAMI; PROPAGATION; SIMULATION; INFERENCE;
   WAVES},
Research-Areas = {Oceanography},
Web-of-Science-Categories  = {Oceanography},
Author-Email = {cdenamie@izor.hr},
Affiliations = {Croatian Institute of Oceanography \& Fisheries (IZOR); University of
   Michigan System; University of Michigan; Universite de Toulon},
ResearcherID-Numbers = {Denamiel, Clea Lumina/AAY-3909-2021
   Vilibic, Ivica/AAE-5160-2019
   Sepic, Jadranka/HPF-2045-2023
   Huan, Xun/A-3025-2017},
ORCID-Numbers = {Denamiel, Clea Lumina/0000-0002-5099-1143
   Sepic, Jadranka/0000-0002-5624-1351
   Huan, Xun/0000-0001-6544-2764},
Funding-Acknowledgement = {project MESSI (UKF) {[}25/15]; project ADIOS (Croatian Science
   Foundation) {[}IP-2016-061955]; ECMWF Special Project (The Adriatic
   decadal and inter-annual oscillations: modelling component)},
Funding-Text = {Acknowledgement is made for the support of the ECMWF staff, in
   particular Xavier Abellan, as well as for ECMWF's computing and archive
   facilities used in this research, which has been supported by projects
   MESSI (UKF Grant 25/15), ADIOS (Croatian Science Foundation Grant
   IP-2016-061955), and ECMWF Special Project (The Adriatic decadal and
   inter-annual oscillations: modelling component). The authors would also
   like to thank the two anonymous reviewers for their valuable
   contributions. The MATLAB interface developed for the stochastic
   surrogate model, including the gPCE coefficients needed to create the
   meteotsunami maximum elevation distributions at the five studied
   locations, as well as the WRF 1.5-km filtered results of sea surface
   pressure can be obtained under the Open Science Framework (OSF) FAIR
   data repository at https://osf.io/jysqu/(doi:10.17605/OSF.IO/JYSQU).},
Number-of-Cited-References = {49},
Times-Cited = {21},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {5},
Journal-ISO = {J. Geophys. Res.-Oceans},
Doc-Delivery-Number = {JZ9DR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000499546200001},
OA = {Green Submitted, Bronze},
DA = {2024-01-15},
}

@article{ WOS:000450722200010,
Author = {Sovilla, B. and McElwaine, J. N. and Kohler, A.},
Title = {The Intermittency Regions of Powder Snow Avalanches},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE},
Year = {2018},
Volume = {123},
Number = {10},
Pages = {2525-2545},
Month = {OCT},
Abstract = {Powder snow avalanches are typically composed of several regions
   characterized by different flow regimes. These include a turbulent
   suspension cloud of fine particles, a dense basal flow, and an
   intermittency frontal region, which is characterized by large
   fluctuations in impact pressure, air pressure, velocity, and density,
   but whose origin remains unknown. In order to describe the physical
   processes governing the intermittency region, we present data from four
   large powder snow avalanches measured at the Vallee de la Sionne test
   site in Switzerland, which show that the intermittency is caused by
   mesoscale coherent structures. These structures have a length of 3-14m
   and a height of 10m or more. The structures can have velocities as much
   as 60\% larger than the avalanche front speed and are characterized by
   an air/particle mixture whose average density can be as high as
   20kg/m(3). This average density increases the drag on large granules by
   a factor of up to 20 compared to pure air, so that each structure can
   maintain denser snow clusters and single snow granules in suspension for
   several seconds. The intermittency region has importance for the
   dynamics of an avalanche, as it provides an efficient mechanism for
   moving snow from the dense layer to the powder cloud, but also for risk
   assessment, as it can cause large forces at large heights above the
   basal dense layer.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Sovilla, B (Corresponding Author), WSL Inst Snow \& Avalanche Res SLF, Davos, Switzerland.
   Sovilla, B.; Kohler, A., WSL Inst Snow \& Avalanche Res SLF, Davos, Switzerland.
   McElwaine, J. N., Univ Durham, Dept Earth Sci, Sci Labs, Durham, England.},
DOI = {10.1029/2018JF004678},
ISSN = {2169-9003},
EISSN = {2169-9011},
Keywords = {powder snow avalanches; mesoscale coherent structures; intermittency
   regime},
Keywords-Plus = {IMPACT-PRESSURE; FLOW; TURBULENT; RADAR; DRY; ENTRAINMENT; DYNAMICS;
   DENSITY; VALLEE; ENERGY},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {sovilla@slf.ch},
Affiliations = {Swiss Federal Institutes of Technology Domain; Swiss Federal Institute
   for Forest, Snow \& Landscape Research; Durham University},
ResearcherID-Numbers = {McElwaine, Jim N/F-1017-2013
   },
ORCID-Numbers = {McElwaine, Jim N/0000-0002-6292-2014
   Sovilla, Betty/0000-0001-8771-6439
   Kohler, Anselm/0000-0001-7431-0691},
Funding-Acknowledgement = {Swiss National Science Foundation (SNSF) {[}200021\_143435]; SNSF
   R'EQUIP project Snow Avalanches in the Swiss experiment
   {[}206021\_113069/1]; canton of Valais; Horizon 2020 project OpenAIRE;
   Swiss National Science Foundation (SNF) {[}200021\_143435] Funding
   Source: Swiss National Science Foundation (SNF)},
Funding-Text = {The authors would like to thank the avalanche dynamics team and
   logistics staff of the WSL/SLF for their support in the experiments. We
   are grateful to Michel Louge for designing of the density sensors and
   for invaluable discussions on powder avalanche dynamics and to Melissa
   Dawes for the language editing. The research was partially funded by the
   Swiss National Science Foundation (SNSF) project High Resolution Radar
   Imaging of Snow Avalanches, grant 200021\_143435, and founding for the
   test site and infrastructure was provided by the SNSF R'EQUIP project
   Snow Avalanches in the Swiss experiment, grant 206021\_113069/1 and by
   the canton of Valais. We gratefully thank Dieter Issler and two
   anonymous reviewers whose suggestions helped improve and clarify this
   manuscript. The data presented in this paper are available in the open
   access data repository Zenodo, which is financed by the Horizon 2020
   project OpenAIRE and hosted by CERN. The associated entry can be
   accessed via B. Sovilla, J. N. McElwaine, and A. Kohler (2018), The
   intermittency regions of powder snow avalanches {[}Data set]. Zenodo.
   https://doi.org/10.5281/zenodo.1415456.},
Number-of-Cited-References = {49},
Times-Cited = {16},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {J. Geophys. Res.-Earth Surf.},
Doc-Delivery-Number = {HB0QN},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000450722200010},
OA = {Green Accepted, hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000464653200002,
Author = {Eshel, Gidon and Dayalu, Archana and Wofsy, Steven C. and Munger, J.
   William and Tziperman, Eli},
Title = {Listening to the Forest: An Artificial Neural Network-Based Model of
   Carbon Uptake at Harvard Forest},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-BIOGEOSCIENCES},
Year = {2019},
Volume = {124},
Number = {3},
Pages = {461-478},
Month = {MAR},
Abstract = {The terrestrial biosphere strongly modulates atmospheric CO2 mixing
   ratios, whose inexorable rise propels anthropogenic climate change.
   Modeling and mechanistically understanding C uptake by the terrestrial
   biosphere are thus of broad societal concerns. Yet despite considerable
   progress, scaling up point observations to landscape and larger scales
   continues to frustrate analyses of the anthropogenically perturbed
   global C cycle. While that up-scaling is our overarching motivation,
   here we focus on one of its elements, modeling C uptake at a given site.
   We devise a novel artificial neural network (ANN)-based model of C
   uptake at Harvard Forest that combines locally observed and remotely
   sensed variables. Most of our model predictors are those used by an
   established ecosystem C uptake model, the Vegetation Photosynthesis and
   Respiration Model (VPRM), easing comparisons. To those, we add observed
   cumulative antecedent precipitation and soil temperature. We find that
   model errors are much larger in winter, indicating that better
   understanding and modeling of respiration will likely discernibly
   improve model performance. Comparing the ANN and VPRM results reveals
   errors attributed to unrealistic treatment of temperature in the VPRM
   formulation, indicating that better representation of temperature
   dependencies is also likely to enhance model skill. By judiciously
   comparing VPRM and ANN errors we thus overcome ANNs' notoriety for
   concealing the mechanisms underlying their predictive skills. We
   demonstrate their ability to identify outstanding ecosystem science
   knowledge gaps and particularly fruitful corresponding model development
   directions, improving site specific and up-scaling flux modeling and
   understanding of the climate impacts of the northern forest.
   Plain Language Summary Anthropogenic climate change due to atmospheric
   carbon dioxide (CO2) buildup reflecting imbalances between emissions and
   uptake is a key challenge. Unfortunately, understanding photosynthetic C
   uptake by land biomes, our focus, is incomplete. The central source of
   insights into this uptake is a network of exchange measuring towers.
   However, this sparse network undersamples the ecosystems they strive to
   represent. Better understanding land C uptake thus depends on vegetation
   models that can upscale local C uptake to regional and global scales. To
   this end, we develop an artificial neural network (ANN) model of C
   uptake in a northern mixed forest measurement site in Massachusetts
   which reduces errors by the equivalent of the emissions of 5.5 million
   Americans. This ANN can be readily applied to any observed terrestrial C
   uptake record at a particular biome, or to all simultaneously. Coupling
   it to a geographically explicit model for filling spacetime gaps thus
   achieves the quest for a spatiotemporally complete land C uptake
   modeling. Our results can also guide future model development by
   identifying error sources. For example, we identify the representation
   of respiration and temperature dependence as promising avenues for
   future research, demonstrating the unique role of ANNs in improving land
   C uptake modeling.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Eshel, G (Corresponding Author), Bard Coll, Phys Dept, Annandale on Hudson, NY 12504 USA.
   Eshel, Gidon, Bard Coll, Phys Dept, Annandale on Hudson, NY 12504 USA.
   Dayalu, Archana; Wofsy, Steven C.; Munger, J. William; Tziperman, Eli, Harvard Univ, Dept Earth \& Planetary Sci, 20 Oxford St, Cambridge, MA 02138 USA.
   Dayalu, Archana; Wofsy, Steven C.; Munger, J. William; Tziperman, Eli, Harvard Univ, Sch Engn \& Appl Sci, Cambridge, MA 02138 USA.},
DOI = {10.1029/2018JG004791},
ISSN = {2169-8953},
EISSN = {2169-8961},
Keywords = {terrestrial biosphere; carbon uptake; neural networks; North America;
   deciduous forest; carbon cycle modeling},
Keywords-Plus = {EDDY-COVARIANCE; EXCHANGE; RESPIRATION; DIOXIDE; FLUXES; CO2;
   PHOTOSYNTHESIS; PRODUCTIVITY; CONVERGENCE; PROJECTIONS},
Research-Areas = {Environmental Sciences \& Ecology; Geology},
Web-of-Science-Categories  = {Environmental Sciences; Geosciences, Multidisciplinary},
Author-Email = {geshel@gmail.com},
Affiliations = {Harvard University; Harvard University},
ResearcherID-Numbers = {Munger, J William/H-4502-2013
   Tziperman, Eli/A-1219-2008
   },
ORCID-Numbers = {Munger, J William/0000-0002-1042-8452
   Wofsy, Steven/0000-0002-3133-2089
   Tziperman, Eli/0000-0002-7998-5775
   Dayalu, Archana/0000-0001-8663-9646},
Funding-Acknowledgement = {National Aeronautics and Space Administration Habitable Worlds programme
   {[}FP062796-A]; U.S. Department of Energy's Office of Science
   {[}DE-AC02-05CH11231]; National Science Foundation {[}DEB-1237491]},
Funding-Text = {E.T. has been funded by National Aeronautics and Space Administration
   Habitable Worlds programme (grant FP062796-A) and thanks the Weizmann
   Institute for its hospitality during parts of this work. G.E. thanks
   Harvard University and its Radcliffe Institute for Advanced Studies for
   their generosity and hospitality during his Radcliffe Fellowship year.
   OSSperation of the Harvard Forest flux tower site is supported by the
   AmeriFlux Management Project with funding by the U.S. Department of
   Energy's Office of Science under contract DE-AC02-05CH11231, and
   additionally as a part of the Harvard Forest LTER site supported by the
   National Science Foundation (DEB-1237491). All relevant code and data
   are archived and wiki documented on the Center for Open Science web site
   at https://osf.io/kjqva/?view\_only= 238b7e65c7394d3fa40c8b32f7bbb075,
   doi:10.17605/OSF.IO/KJQVA. The tower flux data are from Munger and Wofsy
   (2017), available at https://portal.lternet.edu/nis/mapbrowse?
   packageid= knb-lter-hfr.4.28, doi:
   10.6073/pasta/dd9351a3ab5316c844848c3505a8149d. The soil temperature
   data are from the hf005-04 data set of the Harvard Forest data
   repository, available from
   http://harvardforest.fas.harvard.edu:8080/exist/apps/datasets/showData.h
   tml?id=hf005, doi: 10.6073/pasta/cea45e7fb060024359907b2da691b55a.The
   precipitation data are the hf001-06 set {[}entitled ``daily (metric)
   since 2001{''}], also from the Harvard Forest data repository, available
   from http://harvardforest.fas.harvard.edu:
   8080/exist/apps/datasets/showData.html?id= hf001, doi:
   10.6073/pasta/04076dfd30b286c6c29301b6345a63f5. The surface reflectance
   data are from the Terra MOD09A1 MODIS Surface Reflectance 8-Day L3
   Global 500 m SIN Grid V006 data set available at
   https://modis.gsfc.nasa.gov/data/dataprod/mod09.php,
   doi:10.5067/MODIS/MOD09A1.006.E.T. has been funded by National
   Aeronautics and Space Administration Habitable Worlds programme (grant
   FP062796-A) and thanks the Weizmann Institute for its hospitality during
   parts of this work. G.E. thanks Harvard University and its Radcliffe
   Institute for Advanced Studies for their generosity and hospitality
   during his Radcliffe Fellowship year. Operation of the Harvard Forest
   flux tower site is supported by the AmeriFlux Management Project with
   funding by the U.S. Department of Energy's Office of Science under
   contract DE-AC02-05CH11231, and additionally as a part of the Harvard
   Forest LTER site supported by the National Science Foundation
   (DEB-1237491). All relevant code and data are archived and wiki
   documented on the Center for Open Science web site at
   https://osf.io/kjqva/?view\_only= 238b7e65c7394d3fa40c8b32f7bbb075,
   doi:10.17605/OSF.IO/KJQVA. The tower flux data are from Munger and Wofsy
   (2017), available at https://portal.lternet.edu/nis/mapbrowse?
   packageid= knb-lter-hfr.4.28,doi:
   10.6073/pasta/dd9351a3ab5316c844848c3505a8149d. The soil temperature
   data are from the hf005-04 data set of the Harvard Forest data
   repository, available from
   http://harvardforest.fas.harvard.edu:8080/exist/apps/datasets/showData.h
   tml?id=hf005, doi: 10.6073/pasta/cea45e7fb060024359907b2da691b55a.The
   precipitation data are the hf001-06 set {[}entitled ``daily (metric)
   since 2001{''}], also from the Harvard Forest data repository, available
   from http://harvardforest.fas.harvard.edu:
   8080/exist/apps/datasets/showData.html?id= hf001, doi:
   10.6073/pasta/04076dfd30b286c6c29301b6345a63f5. The surface reflectance
   data are from the Terra MOD09A1 MODIS Surface Reflectance 8-Day L3
   Global 500 m SIN Grid V006 data set available at
   https://modis.gsfc.nasa.gov/data/dataprod/mod09.; r php,
   doi:10.5067/MODIS/MOD09A1.006.E.T. has been funded by National
   Aeronautics and Space Administration Habitable Worlds programme (grant
   FP062796-A) and thanks the Weizmann Institute for its hospitality during
   parts of this work. G.E. thanks Harvard University and its Radcliffe
   Institute for Advanced Studies for their generosity and hospitality
   during his Radcliffe Fellowship year. Operation of the Harvard Forest
   flux tower site is supported by the AmeriFlux Management Project with
   funding by the U.S. Department of Energy's Office of Science under
   contract DE-AC02-05CH11231, and additionally as a part of the Harvard
   Forest LTER site supported by the National Science Foundation
   (DEB-1237491). All relevant code and data are archived and wiki
   documented on the Center for Open Science web site at
   https://osf.io/kjqva/?view\_only= 238b7e65c7394d3fa40c8b32f7bbb075,
   doi:10.17605/OSF.IO/KJQVA. The tower flux data are from Munger and Wofsy
   (2017), available at https://portal.lternet.edu/nis/mapbrowse?
   packageid= knb-lter-hfr.4.28,doi:
   10.6073/pasta/dd9351a3ab5316c844848c3505a8149d. The soil temperature
   data are from the hf005-04 data set of the Harvard Forest data
   repository, available from
   http://harvardforest.fas.harvard.edu:8080/exist/apps/datasets/showData.h
   tml?id=hf005, doi: 10.6073/pasta/cea45e7fb060024359907b2da691b55a.The
   precipitation data are the hf001-06 set {[}entitled ``daily (metric)
   since 2001{''}], also from the Harvard Forest data repository, available
   from http://harvardforest.fas.harvard.edu:
   8080/exist/apps/datasets/showData.html?id= hf001, doi:
   10.6073/pasta/04076dfd30b286c6c29301b6345a63f5. The surface reflectance
   data are from the Terra MOD09A1 MODIS Surface Reflectance 8-Day L3
   Global 500 m SIN Grid V006 data set available at
   https://modis.gsfc.nasa.gov/data/dataprod/mod09.php,doi:10.5067/MODIS/MO
   D09A1.006.E.T. has been funded by National Aeronautics and Space
   Administration Habitable Worlds programme (grant FP062796-A) and thanks
   the Weizmann Institute for its hospitality during parts of this work.
   G.E. thanks Harvard University and its Radcliffe Institute for Advanced
   Studies for their generosity and hospitality during his Radcliffe
   Fellowship year. Operation of the Harvard Forest flux tower site is
   supported by the AmeriFlux Management Project with funding by the U.S.
   Department of Energy's Office of Science under contract
   DE-AC02-05CH11231, and additionally as a part of the Harvard Forest LTER
   site supported by the National Science Foundation (DEB-1237491). All
   relevant code and data are archived and wiki documented on the Center
   for Open Science web site at https://osf.io/kjqva/?view\_only=
   238b7e65c7394d3fa40c8b32f7bbb075, doi:10.17605/OSF.IO/KJQVA. The tower
   flux data are from Munger and Wofsy (2017), available at
   https://portal.lternet.edu/nis/mapbrowse? packageid=
   knb-lter-hfr.4.28,doi: 10.6073/pasta/dd9351a3ab5316c844848c3505a8149d.
   The soil temperature data are from the hf005-04 data set of the Harvard
   Forest data repository, available from
   http://harvardforest.fas.harvard.edu:8080/exist/apps/datasets/showData.h
   tml?id=hf005, doi: 10.6073/pasta/cea45e7fb060024359907b2da691b55a.The
   precipitation data are the hf001-06 set {[}entitled ``daily (metric)
   since 2001{''}], also from the Harvard Forest data repository, available
   from http://harvardforest.fas.harvard.edu:
   8080/exist/apps/datasets/showData.html?id= hf001, doi:
   10.6073/pasta/04076dfd30b286c6c29301b6345a63f5. The surface reflectance
   data are from the Terra MOD09A1 MODIS Surface Reflectance 8-Day L3
   Global 500 m SIN Grid V006 data set available at https://modis.gsfc.; r
   nasa.gov/data/dataprod/mod09.php, doi:10.5067/MODIS/MOD09A1.006.},
Number-of-Cited-References = {62},
Times-Cited = {4},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {29},
Journal-ISO = {J. Geophys. Res.-Biogeosci.},
Doc-Delivery-Number = {HT6DA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000464653200002},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000496185900001,
Author = {Kim, Jae-Seung and Seo, Ki-Weon and Jeon, Taehwan and Chen, Jianli and
   Wilson, Clark R.},
Title = {Missing Hydrological Contribution to Sea Level Rise},
Journal = {GEOPHYSICAL RESEARCH LETTERS},
Year = {2019},
Volume = {46},
Number = {21},
Pages = {12049-12055},
Month = {NOV 16},
Abstract = {Over the past decade, the rate of global mean sea level (GMSL) rise is
   about 3.5 mm/year. Terrestrial water/ice mass loss to the oceans and
   ocean volume expansion explain about 3.1 mm/year, indicating that the
   GMSL budget is not been fully understood. Past estimates from Gravity
   Recovery and Climate Experiment (GRACE) data have indicated that
   terrestrial water storage (TWS) is increasing and is thus a mitigating
   contributor to GMSL rise. However, TWS estimates from GRACE are
   uncertain mostly due to limitations in GRACE estimates of degree-1 and
   degree-2 order-0 spherical harmonic coefficients. We obtain an improved
   estimate of the TWS contribution to GMSL change using revised GRACE
   estimates of these low-degree coefficients. For the period 2005-2015, we
   find that TWS makes an additional contribution to GMSL rise of about
   0.32 +/- 0.02 mm/year, mostly associated with a TWS decrease. This
   revised estimate is sufficient to nearly balance the budget of GMSL
   rise.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Seo, KW (Corresponding Author), Seoul Natl Univ, Dept Earth Sci Educ, Seoul, South Korea.
   Seo, KW (Corresponding Author), Univ Texas Austin, Ctr Space Res, Austin, TX 78712 USA.
   Kim, Jae-Seung; Seo, Ki-Weon; Jeon, Taehwan, Seoul Natl Univ, Dept Earth Sci Educ, Seoul, South Korea.
   Seo, Ki-Weon; Chen, Jianli; Wilson, Clark R., Univ Texas Austin, Ctr Space Res, Austin, TX 78712 USA.
   Wilson, Clark R., Univ Texas Austin, Dept Geol Sci, Jackson Sch Geosci, Austin, TX USA.},
DOI = {10.1029/2019GL085470},
EarlyAccessDate = {NOV 2019},
ISSN = {0094-8276},
EISSN = {1944-8007},
Keywords = {sea level rise; GRACE; terrestrial water storage},
Keywords-Plus = {ICE-SHEET; MASS CHANGES; GRACE; BUDGET; MODEL; 20TH-CENTURY; BALANCE},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {seokiweon@snu.ac.kr},
Affiliations = {Seoul National University (SNU); University of Texas System; University
   of Texas Austin; University of Texas System; University of Texas Austin},
ResearcherID-Numbers = {Seo, Ki-weon/AAH-7729-2021
   },
ORCID-Numbers = {Seo, Ki-weon/0000-0001-5523-4996
   Kim, Jae-Seung/0000-0001-7911-7858
   Chen, Jianli/0000-0001-5405-8441
   Wilson, Clark/0000-0003-1288-3245},
Funding-Acknowledgement = {Korea Institute of Marine Science and Technology Promotion (KIMST)
   {[}KIMST20190361, PM19020]; NASA GRACE Project {[}NNL14AA00C]; NASA ESI
   Program {[}NNX12AM86G, NNX17AG96G]; NASA {[}NNX12AM86G, 69722] Funding
   Source: Federal RePORTER},
Funding-Text = {This study was supported by the Korea Institute of Marine Science and
   Technology Promotion (KIMST) research grant (KIMST20190361; PM19020).
   J.C. was supported by the NASA GRACE Project (under contract NNL14AA00C)
   and NASA ESI Program (NNX12AM86G and NNX17AG96G). CSR, GFZ, and JPL RL06
   GRACE data can be downloaded at
   https://podaac.jpl.nasa.gov/dataaccess.SLR. Delta C20 and PGR model of
   A13 are available at GRACE Tellus website
   (https://grace.jpl.nasa.gov/data/get-data/). PGR model of Caron18 can be
   downloaded at
   https://vesl.jpl.nasa.gov/solid-earth/gia/downloads/GIA\_present\_day\_
   grid\_file.txt, and Peltier18 can be accessed from Dr. Peltier's website
   (http://www.atmosp.physics.utoronto.ca/peltier/data.php). The data that
   support the findings of this study are available from a data repository
   of Open Science Framework (https://doi.org/10.17605/OSF.IO/XNS48).},
Number-of-Cited-References = {41},
Times-Cited = {19},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {9},
Journal-ISO = {Geophys. Res. Lett.},
Doc-Delivery-Number = {JU5NV},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000496185900001},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000447858800037,
Author = {Pourpoint, Maeva and Anandakrishnan, Sridhar and Ammon, Charles J. and
   Alley, Richard B.},
Title = {Lithospheric Structure of Greenland From Ambient Noise and Earthquake
   Surface Wave Tomography},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SOLID EARTH},
Year = {2018},
Volume = {123},
Number = {9},
Pages = {7850-7876},
Month = {SEP},
Abstract = {We present a high-resolution shear wave velocity model of Greenland's
   lithosphere from regional and teleseismic Rayleigh waves recorded by the
   Greenland Ice Sheet Monitoring Network supplemented with observations
   from several temporary seismic deployments. To construct Rayleigh wave
   group velocity maps, we integrated signals from regional and teleseismic
   earthquakes with several years of ambient seismic noise and used the
   dispersion to constrain crustal and upper-mantle seismic shear wave
   velocity structure. Specifically, we used a Markov Chain Monte Carlo
   technique to estimate 3-D shear wave velocities beneath Greenland to a
   depth of 200km. Our model reveals four prominent anomalies: a deep
   high-velocity feature extending from southwestern to northwestern
   Greenland that may be the signature of a thick cratonic keel, a corridor
   of relatively low upper-mantle velocity across central Greenland that
   could be associated with lithospheric modification from the passage of
   the Iceland plume beneath Greenland or interpreted as a tectonic
   boundary between cratonic blocks, an upper-crustal southwest-northeast
   trending boundary separating Greenland into two regions of contrasting
   tectonic and crustal properties, and a midcrustal low-velocity anomaly
   beneath northeastern Greenland. The nature of this midcrustal anomaly is
   of particular interest given that it underlies the onset of the
   Northeast Greenland Ice Stream and raises interesting questions
   regarding how deeper processes may impact the ice stream dynamics and
   the evolution of the Greenland Ice Sheet.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Pourpoint, M (Corresponding Author), Washington Univ, Dept Earth \& Planetary Sci, St Louis, MO 63130 USA.
   Pourpoint, Maeva, Washington Univ, Dept Earth \& Planetary Sci, St Louis, MO 63130 USA.
   Anandakrishnan, Sridhar; Ammon, Charles J.; Alley, Richard B., Penn State Univ, Dept Geosci, University Pk, PA 16802 USA.},
DOI = {10.1029/2018JB015490},
ISSN = {2169-9313},
EISSN = {2169-9356},
Keywords = {Surface wave tomography; Lithospheric Structure; Greenland; Iceland
   plume track; Crustal low velocity anomaly},
Keywords-Plus = {CRUSTAL STRUCTURE; EAST GREENLAND; UPPER-MANTLE; NORTH-ATLANTIC; THERMAL
   STRUCTURE; WEST GREENLAND; BASAL MELT; HEAT-FLOW; ICE; VELOCITY},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {pourpointmaeva@gmail.com},
Affiliations = {Washington University (WUSTL); Pennsylvania Commonwealth System of
   Higher Education (PCSHE); Pennsylvania State University; Pennsylvania
   State University - University Park},
ResearcherID-Numbers = {Anandakrishnan, Sridhar/JCN-5026-2023
   },
ORCID-Numbers = {Pourpoint, Maeva/0000-0003-3537-9770
   Alley, Richard/0000-0003-1833-0115},
Funding-Acknowledgement = {U.S. National Science Foundation {[}EAR-1246776, AGS-1338832]; Defense
   Threat Reduction Agency award {[}HDTRA1-11-1-0027]; National Science
   Foundation through the Instrumentation; Facilities Program of the
   National Science Foundation {[}EAR-1063471]},
Funding-Text = {This work was supported by the U.S. National Science Foundation (grants
   EAR-1246776 {[}partial M.P. and S.Al and AGS-1338832 {[}R.A. and S.Al)
   and by the Defense Threat Reduction Agency award HDTRA1-11-1-0027
   (partial M.P. and C. A.). The time series and metadata used in this
   study are open access and available through the facilities of the IRIS
   DMC (IRIS Data Management System). When available, the DOT's for
   permanent and temporary networks used in this study have also been
   listed in the references (Albuquerque Seismological Laboratory
   (ASL)/USGS, 1988; GEOFON Data Centre, 1993; GEOSCOPE, 1982; Korea Polar
   Research Institute (KOPRI), 2013; Scripps Institution of Oceanography,
   1986). IRIS is funded through the National Science Foundation through
   the Instrumentation and Facilities Program of the National Science
   Foundation under cooperative agreement EAR-1063471. The National
   Earthquake Information Center Advanced National Seismic System
   Comprehensive Catalog and the Global Centroid Moment Tensor Project
   Catalog were used to construct lists of earthquakes used in our
   analyses. A list of the regional and teleseismic events used to build
   our earthquake tomography model and our final 3-D shear wave velocity
   model (median model) are available in a digital form on the figshare
   data repository (doi:10.6084/m9.figshare.6291074).},
Number-of-Cited-References = {134},
Times-Cited = {15},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {14},
Journal-ISO = {J. Geophys. Res.-Solid Earth},
Doc-Delivery-Number = {GX6GP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000447858800037},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000490956600008,
Author = {Khazanov, V, George and Chen, Margaret W. and Lemon, Colby L. and
   Sibeck, David G.},
Title = {The Magnetosphere-Ionosphere Electron Precipitation Dynamics and Their
   Geospace Consequences During the 17 March 2013 Storm},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2019},
Volume = {124},
Number = {8},
Pages = {6504-6523},
Month = {AUG},
Abstract = {During geomagnetic storms and substorms, the magnetosphere and
   ionosphere are strongly coupled by precipitating magnetospheric
   electrons from the Earth's plasma sheet and driven by both
   magnetospheric and ionospheric processes. Magnetospheric wave activity
   initiates electron precipitation, and the ionosphere and upper
   atmosphere further facilitate this process by enhancing the value of
   precipitated energy fluxes via connection of two magnetically conjugate
   regions and multiple atmospheric reflections. This paper focuses on the
   resulting electron energy fluxes and affiliated height-integrated
   Pedersen and Hall conductances in the auroral regions produced by
   multiple atmospheric reflections during the 17 March 2013 geomagnetic
   storm and their effects on the inner magnetospheric electric field and
   ring current. Our study is based on the magnetically and electrically
   self-consistent Rice Convection Model-Equilibrium of the inner
   magnetosphere with SuperThermal Electron Transport modified electron
   energy fluxes that take into account the electron energy interplay
   between the two magnetically conjugate ionospheres. SuperThermal
   Electron Transport-modified energy flux in the Rice Convection
   Model-Equilibrium leads to a significant difference in the global
   conductance pattern, ionospheric electric field formation, Birkeland
   current structure, ring current energization and its energy content,
   subauroral polarization drifts intensifications and their spatial
   locations, interchange instability redistribution, and overall energy
   interplay on the global scale.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Khazanov, GV (Corresponding Author), NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA.
   Khazanov, George, V; Sibeck, David G., NASA, Goddard Space Flight Ctr, Greenbelt, MD 20771 USA.
   Chen, Margaret W.; Lemon, Colby L., Aerosp Corp, El Segundo, CA 90245 USA.},
DOI = {10.1029/2019JA026589},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords = {storm; precipitation; conductance; electric field; ring current; SAPS},
Keywords-Plus = {RING CURRENT SIMULATIONS; DIFFUSE AURORA; INTERCHANGE INSTABILITY;
   ENERGY CONTENT; MODEL; SUBSTORM; CONDUCTANCES; REGIONS; MORPHOLOGY;
   RATES},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {george.v.khazanov@nasa.gov},
Affiliations = {National Aeronautics \& Space Administration (NASA); NASA Goddard Space
   Flight Center; Aerospace Corporation - USA},
ResearcherID-Numbers = {Sibeck, David G/D-4424-2012
   Chen, Margaret W/C-9658-2013
   },
ORCID-Numbers = {Chen, Margaret W/0000-0001-7771-4771
   Lemon, Colby/0000-0002-2189-5769},
Funding-Acknowledgement = {NASA {[}NNX16AG72G, NNX14AF35G, NNX16AH46G, NNH14ZDA001N-HSR
   MAG14\_2-0062]; NASA Heliophysics Internal Scientist Funding Models
   {[}HISFM18-0006, HISFM18-0009]; NASA LWS Program {[}80NSSC19K0080]; NSF
   {[}AGS 1602862]; Aerospace Technical Investment Program; NASA Van Allen
   Probes Project; NASA {[}683497, NNX14AF35G, 904226, NNX16AG72G,
   NNX16AH46G, 904184] Funding Source: Federal RePORTER},
Funding-Text = {The OMNI data used as input for the RCM-E simulations were obtained from
   the GSFC/SPDF OMNIWeb interface (http://omniweb.gsfc.nasa.gov).We thank
   numerous geomagnetic observatories (Kakioka {[}JMA], Honolulu and San
   Juan {[}USGS], Hermanus {[}RSA], Alibag {[}IIG], NiCT, INTERMAGNET, and
   many others) for their cooperation in making the SYM-H index available.
   The SYM-H data, STET data for the analytical fits, and simulation data
   used to make the figures in this study are available at the Open Science
   Framework data repository (https://osf.io/5t4dr/and
   http://doi.org/10.5281/zenodo.1206051).G.V.K.was supported by NASA Grant
   NNH14ZDA001N-HSR MAG14\_2-0062, NASA Heliophysics Internal Scientist
   Funding Models (HISFM18-0006 and HISFM18-0009), NASA Van Allen Probes
   Project, and NASA LWS Program under the Award 80NSSC19K0080. The
   research of M. W. C. and C. L. L. at The Aerospace Corporation was
   supported by the NASA Grants NNX16AG72G, NNX14AF35G, and NNX16AH46G (C.
   L. L. only), NSF Grant AGS 1602862, and the Aerospace Technical
   Investment Program.},
Number-of-Cited-References = {68},
Times-Cited = {13},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {3},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {JE8RD},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000490956600008},
OA = {Bronze},
DA = {2024-01-15},
}

@article{ WOS:000548601000026,
Author = {Nelson, A. D. and Arbic, B. K. and Menemenlis, D. and Peltier, W. R. and
   Alford, M. H. and Grisouard, N. and Klymak, J. M.},
Title = {Improved Internal Wave Spectral Continuum in a Regional Ocean Model},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-OCEANS},
Year = {2020},
Volume = {125},
Number = {5},
Month = {MAY},
Abstract = {Recent work demonstrates that high-resolution global models forced
   simultaneously by atmospheric fields and the astronomical tidal
   potential contain a partial internal (gravity) wave (IW) spectral
   continuum. Regional simulations of the MITgcm forced at the horizontal
   boundaries by a global run that carries a partial IW continuum spectrum
   are performed at the same grid spacing as the global run and at finer
   grid spacings in an attempt to fill out more of the IW spectral
   continuum. Decreasing only the horizontal grid spacing from 2 to 0.25km
   greatly improves the frequency spectra and slightly improves the
   vertical wavenumber spectra of the horizontal velocity. Decreasing only
   the vertical grid spacing by a factor of 3 does not yield any
   significant improvements. Decreasing both horizontal and vertical grid
   spacings yields the greatest degree of improvement, filling the
   frequency spectrum out to 72cpd. Our results suggest that improved IW
   spectra in regional models are possible if they are run at finer grid
   spacings and are forced at their lateral boundaries by remotely
   generated IWs. Additionally, consistency relations demonstrate that
   improvements in the spectra are indeed due to the existence of IWs at
   higher frequencies and vertical wavenumbers when remote IW forcing is
   included and model grid spacings decrease. By being able to simulate an
   IW spectral continuum to 0.25km scales, these simulations demonstrate
   that one may be able to track the energy pathways of IWs from generation
   to dissipation and improve the understanding of processes such as
   IW-driven mixing.
   Plain Language Summary Models of internal waves (IWs) may help us to
   better understand the spatial geography of mixing in the ocean and are
   playing an increasingly important role in the planning of satellite
   missions. Following recent work showing that high-resolution global
   models contain a partial IW spectrum, this paper describes further
   improvements in the spectrum seen in a high-resolution regional model
   forced at the boundaries by a previously performed global IW simulation.
   Decreasing only the horizontal grid spacing greatly improves the
   frequency spectra and slightly improves the vertical wavenumber spectra
   of velocity. Increasing only the number of vertical levels does not
   yield any significant improvements. Decreasing both horizontal and
   vertical grid spacings yields the greatest improvement in both spectra.
   Our results suggest that regional models can exhibit improved IW spectra
   over global models if two conditions are met-they must have higher
   horizontal and vertical resolutions, and they must have remotely
   generated IWs at their boundaries. Application of the so-called
   consistency relations demonstrates that the model is indeed carrying a
   field of high-frequency IWs. Being able to simulate a fuller IW spectrum
   demonstrates that one may be able to use these models to improve the
   understanding of IW-driven processes and energy pathways.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Nelson, AD (Corresponding Author), Univ Michigan, Dept Earth \& Environm Sci, Ann Arbor, MI 48109 USA.
   Nelson, A. D.; Arbic, B. K., Univ Michigan, Dept Earth \& Environm Sci, Ann Arbor, MI 48109 USA.
   Menemenlis, D., CALTECH, Jet Prop Lab, Pasadena, CA USA.
   Peltier, W. R.; Grisouard, N., Univ Toronto, Dept Phys, Toronto, ON, Canada.
   Alford, M. H., Univ Calif San Diego, Scripps Inst Oceanog, La Jolla, CA 92093 USA.
   Klymak, J. M., Univ Victoria, Sch Earth \& Ocean Sci, Victoria, BC, Canada.
   Klymak, J. M., Univ Victoria, Dept Phys \& Astron, Victoria, BC, Canada.},
DOI = {10.1029/2019JC015974},
ISSN = {2169-9275},
EISSN = {2169-9291},
Keywords = {ocean; internal waves; internal wave spectra; ocean models;
   high-resolution modeling; regional modeling},
Keywords-Plus = {SEA-SURFACE HEIGHT; SPACE-TIME SCALES; CONSISTENCY RELATIONS;
   KINETIC-ENERGY; GRAVITY; SIMULATION; RESOLUTION; TIDES},
Research-Areas = {Oceanography},
Web-of-Science-Categories  = {Oceanography},
Author-Email = {dr.adnelson@gmail.com},
Affiliations = {University of Michigan System; University of Michigan; National
   Aeronautics \& Space Administration (NASA); NASA Jet Propulsion
   Laboratory (JPL); California Institute of Technology; University of
   Toronto; University of California System; University of California San
   Diego; Scripps Institution of Oceanography; University of Victoria;
   University of Victoria},
ResearcherID-Numbers = {Menemenlis, Dimitris/G-8091-2017
   Klymak, Jody M/A-3041-2008
   Peltier, William R./A-1102-2008
   Grisouard, Nicolas/A-1892-2012
   },
ORCID-Numbers = {Menemenlis, Dimitris/0000-0001-9940-8409
   Klymak, Jody M/0000-0003-4612-8600
   Grisouard, Nicolas/0000-0003-4045-2143
   Nelson, Arin/0000-0002-1080-8674
   Arbic, Brian K/0000-0002-7969-2294},
Funding-Acknowledgement = {NASA {[}NNX17AH55G, NNX16AH79G]; Natural Sciences and Engineering
   Research Council of Canada {[}A9627]; NSERC {[}RGPIN-2015-03684];
   Canadian Space Agency {[}14SUSWOTTO]; NSF; NASA {[}NNX16AH79G, 904102]
   Funding Source: Federal RePORTER},
Funding-Text = {We first wish to thank the editor and the anonymous reviewers, whose
   contributions significantly strengthened this manuscript. A. D. N. and
   B. K. A. were supported by NASA Grants NNX17AH55G and NNX16AH79G. W. R.
   P. was supported by the Natural Sciences and Engineering Research
   Council of Canada under NSERC Discovery Grant A9627. N. G. was supported
   under NSERC Discovery Grant RGPIN-2015-03684 and Canadian Space Agency
   Grant 14SUSWOTTO. The computations described in this paper were
   performed on the Niagara supercomputer of the SciNet facility of the
   University of Toronto, which is a component of the Compute Canada HPC
   platform. The observations and MMP-sampled modeled data used in this
   study are open-access and hosted at the University of Michigan Deep Blue
   Data repository (at
   https://deepblue.lib.umich.edu/data/concern/data\_sets/9s1616296).The
   MMP observations from Alford et al. (2007) were funded by NSF and used
   with permission and provided by Gunnar Voet at Scripps. The MMP
   observations would not have been possible without the talent and hard
   work of the captain, Tom DesJardines, and crew of R/V Revelle. The
   authors also wish to thank Eric Kunze for insightful discussions about
   the importance of WKBJ stretching and CarlWunsch, Dirk Olbers, and
   Ren-Chieh Lien for suggesting that we test IGWmodels using consistency
   relations.},
Number-of-Cited-References = {43},
Times-Cited = {18},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {6},
Journal-ISO = {J. Geophys. Res.-Oceans},
Doc-Delivery-Number = {MK2FJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000548601000026},
OA = {Green Published, Bronze},
DA = {2024-01-15},
}

@article{ WOS:000439784300019,
Author = {Trugman, A. T. and Medvigy, D. and Mankin, J. S. and Anderegg, W. R. L.},
Title = {Soil Moisture Stress as a Major Driver of Carbon Cycle Uncertainty},
Journal = {GEOPHYSICAL RESEARCH LETTERS},
Year = {2018},
Volume = {45},
Number = {13},
Pages = {6495-6503},
Month = {JUL 16},
Abstract = {Future projections suggest an increase in drought globally with climate
   change. Current vegetation models typically regulate the plant
   photosynthetic response to soil moisture stress through an empirical
   function, rather than a mechanistic response where plant water
   potentials respond to changes in soil water. This representation of soil
   moisture stress may introduce significant uncertainty into projections
   for the terrestrial carbon cycle. We examined the use of the soil
   moisture limitation function in historical and future emissions
   scenarios in nine Earth system models. We found that soil
   moisture-limited productivity across models represented a large and
   uncertain component of the simulated carbon cycle, comparable to 3-286\%
   of current global productivity. Approximately 40-80\% of the intermodel
   variability was due to the functional form of the limitation equation
   alone. Our results highlight the importance of implementing mechanistic
   water limitation schemes in models and illuminate several avenues for
   improving projections of the land carbon sink.
   Plain Language Summary Understanding the environmental controls of
   terrestrial ecosystem productivity is of critical importance because
   terrestrial ecosystems directly impact the concentration of CO2 in the
   atmosphere. However, model projections disagree on the future sign and
   magnitude of terrestrial ecosystem CO2 drawdown, so it is uncertain if
   terrestrial ecosystems will continue to mitigate climate change in the
   future. Here we show that the current representation of water-limited
   productivity across state-of-the-art vegetation models is a large and
   uncertain component of terrestrial productivity, comparable in magnitude
   to current global productivity. Our results provide a foundation for
   improved projections of climate change impacts on terrestrial
   ecosystems, ranging from vegetation growth to agricultural productivity.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Trugman, AT (Corresponding Author), Univ Utah, Dept Biol, Salt Lake City, UT 84112 USA.
   Trugman, A. T.; Anderegg, W. R. L., Univ Utah, Dept Biol, Salt Lake City, UT 84112 USA.
   Medvigy, D., Univ Notre Dame, Dept Biol Sci, Notre Dame, IN 46556 USA.
   Mankin, J. S., Columbia Univ, Lamont Doherty Geol Observ, Div Ocean \& Climate Phys, Palisades, NY 10964 USA.
   Mankin, J. S., Dartmouth Coll, Dept Geog, Hanover, NH 03755 USA.},
DOI = {10.1029/2018GL078131},
ISSN = {0094-8276},
EISSN = {1944-8007},
Keywords = {carbon cycle uncertainty; climate change; soil moisture stress; drought;
   terrestrial carbon cycle; vegetation model},
Keywords-Plus = {SEMIARID ECOSYSTEMS; HYDRAULIC TRAITS; DIOXIDE UPTAKE; CLIMATE;
   VEGETATION; LAND; INCREASE; DROUGHT; VARIABILITY; PROJECTIONS},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {a.trugman@utah.edu},
Affiliations = {Utah System of Higher Education; University of Utah; University of Notre
   Dame; Columbia University; Dartmouth College},
ResearcherID-Numbers = {Mankin, Justin/N-2979-2017
   },
ORCID-Numbers = {Mankin, Justin/0000-0003-2520-4555
   Trugman, Anna/0000-0002-7903-9711},
Funding-Acknowledgement = {USDA National Institute of Food and Agriculture Postdoctoral Research
   Fellowship {[}2017-07164]; National Science Foundation {[}1714972,
   1151102]; University of Utah Global Change and Sustainability Center;
   USDA National Institute of Food and Agriculture, Agricultural and Food
   Research Initiative Competitive Programme, Ecosystem Services and
   Agro-ecosystem Management {[}2017-05521]; U.S. Department of Energy,
   Office of Science, Office of Biological and Environmental Research,
   Terrestrial EcosystemScience (TES) Program {[}DE-SC0014363]; Earth
   Institute; Directorate For Geosciences; Div Atmospheric \& Geospace
   Sciences {[}1733571] Funding Source: National Science Foundation;
   Directorate For Geosciences; Div Atmospheric \& Geospace Sciences
   {[}1151102] Funding Source: National Science Foundation},
Funding-Text = {The authors declare no conflict of interest. We acknowledge the World
   Climate Research Programme's Working Group on Coupled Modeling, which is
   responsible for CMIP, and we thank the climate modeling groups (listed
   in the supporting information) for producing and making available their
   model output. The authors acknowledge support from the USDA National
   Institute of Food and Agriculture Postdoctoral Research Fellowship grant
   2017-07164 to A. T. T.; the National Science Foundation grant 1714972,
   the University of Utah Global Change and Sustainability Center, and the
   USDA National Institute of Food and Agriculture, Agricultural and Food
   Research Initiative Competitive Programme, Ecosystem Services and
   Agro-ecosystem Management, grant 2017-05521 to W. R. L. A.; National
   Science Foundation Award 1151102 and U.S. Department of Energy, Office
   of Science, Office of Biological and Environmental Research, Terrestrial
   EcosystemScience (TES) Program award DE-SC0014363 to D. M.; and the
   Earth Institute to J. S. M. We also thank Steve Pacala for his helpful
   feedback. Lamont Contribution 8228. All CMIP5 multimodel ensemble data
   are available at the Centre for Environmental Data Archival
   (https://services.ceda.ac.uk/). Maps of estimated beta and
   GPP<INF>c</INF> are archived on the Hive, the University of Utah's Open
   Access Institutional Data Repository
   (https://hive.utah.edu/concern/generic\_works/pk02c973d; doi:
   10.7278/S5707ZMS).},
Number-of-Cited-References = {43},
Times-Cited = {104},
Usage-Count-Last-180-days = {15},
Usage-Count-Since-2013 = {80},
Journal-ISO = {Geophys. Res. Lett.},
Doc-Delivery-Number = {GO2FL},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000439784300019},
OA = {Bronze, Green Submitted, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000701351400008,
Author = {Taubenschuss, Ulrich and Lamy, Laurent and Fischer, Georg and Pisa,
   David and Santolik, Ondrej and Soucek, Jan and Kurth, William S. and
   Cecconi, Baptiste and Zarka, Philippe and Rucker, Helmut O.},
Title = {The Faraday rotation effect in Saturn Kilometric Radiation observed by
   the CASSINI spacecraft},
Journal = {ICARUS},
Year = {2021},
Volume = {370},
Month = {DEC},
Abstract = {Non-thermal radio emissions from Saturn, known as Saturn Kilometric
   Radiation (SKR), are analyzed for the Faraday rotation effect detected
   in Cassini RPWS High Frequency Receiver (HFR) observations. This
   phenomenon, which mainly affects the lower-frequency part of SKR below
   200 kHz, is characterized by a rotation of the semi-major axis of the
   SKR polarization ellipse as a function of frequency during wave
   propagation through a birefringent plasma medium. Faraday rotation is
   found in 4.1\% of all HFR data recorded by Cassini above 20 degrees
   northern and southern magnetic latitude, from mid-2004 to late 2017. A
   statistical visibility analysis shows that elliptically polarized SKR
   from the dawn source regions, when beamed toward high latitudes into the
   noon and afternoon local time sectors, is most likely to experience
   Faraday rotation along the ray path. The necessary conditions for
   Faraday rotation are discussed in terms of birefringent media and sharp
   plasma density gradients, where SKR (mostly R-X mode) gets split into
   the two circularly polarized modes R-X and L-O. By means of a case study
   we also demonstrate how Faraday rotation provides an estimate for the
   average plasma density along the ray path.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Taubenschuss, U (Corresponding Author), Czech Acad Sci, Dept Space Phys, Inst Atmospher Phys, Prague, Czech Republic.
   Taubenschuss, Ulrich; Pisa, David; Santolik, Ondrej; Soucek, Jan, Czech Acad Sci, Dept Space Phys, Inst Atmospher Phys, Prague, Czech Republic.
   Santolik, Ondrej, Charles Univ Prague, Fac Math \& Phys, Prague, Czech Republic.
   Lamy, Laurent; Cecconi, Baptiste; Zarka, Philippe, Sorbonne Univ, Univ PSL, Univ Paris, LESIA,Observ Paris,CNRS, Meudon, France.
   Lamy, Laurent, Aix Marseille Univ, LAM, CNES, CNRS, Marseille, France.
   Fischer, Georg, Austrian Acad Sci, Space Res Inst, Graz, Austria.
   Rucker, Helmut O., Austrian Acad Sci, Commiss Astron, Graz, Austria.
   Kurth, William S., Univ Iowa, Dept Phys \& Astron, Iowa City, IA 52242 USA.},
DOI = {10.1016/j.icarus.2021.114661},
EarlyAccessDate = {SEP 2021},
Article-Number = {114661},
ISSN = {0019-1035},
EISSN = {1090-2643},
Keywords = {Cassini; Saturn kilometric radiation; Faraday rotation},
Keywords-Plus = {INHOMOGENEOUS MAGNETIZED PLASMA; AURORAL RADIO EMISSIONS; POLARIZATION;
   FIELD},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {ut@ufa.cas.cz},
Affiliations = {Czech Academy of Sciences; Institute of Atmospheric Physics of the Czech
   Academy of Sciences; Charles University Prague; Centre National de la
   Recherche Scientifique (CNRS); Universite PSL; Observatoire de Paris;
   Universite Paris Cite; Sorbonne Universite; Aix-Marseille Universite;
   Centre National de la Recherche Scientifique (CNRS); Austrian Academy of
   Sciences; Austrian Academy of Sciences; University of Iowa},
ResearcherID-Numbers = {Soucek, Jan/G-3424-2014
   Zarka, Philippe/JSL-2437-2023
   Santolik, Ondrej/F-7766-2014
   Fischer, Georg/Y-3059-2019
   Cecconi, Baptiste/ABF-3912-2020
   Kurth, William/AAA-7334-2019
   Taubenschuss, Ulrich/E-3739-2015
   Pisa, David/H-6314-2014
   },
ORCID-Numbers = {Soucek, Jan/0000-0003-0462-6804
   Santolik, Ondrej/0000-0002-4891-9273
   Fischer, Georg/0000-0002-4033-2005
   Cecconi, Baptiste/0000-0001-7915-5571
   Kurth, William/0000-0002-5471-6202
   Taubenschuss, Ulrich/0000-0003-4810-6958
   Pisa, David/0000-0002-1322-7576
   Fischer, Georg/0000-0002-0431-2381
   Lamy, Laurent/0000-0002-8428-1369},
Funding-Acknowledgement = {CNRS; CNES; ``Agence Nationale de la Recherche, France{''}, ``Programme
   d'Investissements d'Avenir{''} {[}ANR-11-IDEX-000402]; FWF-GACR
   international project, Austria {[}I 4559-N/20-06802L]; Austrian Science
   Fund (FWF) {[}I 4559-N]; CNES, France; CNRS/INSU, France national
   program of planetology and heliophysics},
Funding-Text = {The Cassini/RPWS/HFR LESIA/Kronos N2 (level 2) data collection has been
   produced by B. Cecconi, L. Lamy \& P. Zarka, from the Observatoire de
   Paris/LESIA Cassini-RPWS team, with the support of CNRS and CNES
   (Cecconi et al., 2017a). Cassini trajectory data are provided by the
   Cassini RPWS Team page at
   http://cassini.physics.uiowa.edu/cassini/team/team.html and by the
   Cassini/RPWS/HFR LESIA/Kronos data repository at
   https://lesia.obspm.fr/kronos/data/.A list of all identified Faraday
   rotation events can be accessed at https://doi.org/10.25935/R11G-6J63
   (Taubenschuss et al., 2021). This work has been done partly within the
   LABEX PLAS@PAR project, and received financial state aid managed by the
   ``Agence Nationale de la Recherche, France{''}, as part of the
   ``Programme d'Investissements d'Avenir{''} under the reference
   ANR-11-IDEX-000402. U.T., G.F., D.P., J.S., O.S. and H.O.R. acknowledge
   support from the FWF-GACR international project, Austria I
   4559-N/20-06802L. This research was funded in whole, or in part, by the
   Austrian Science Fund (FWF) {[}I 4559-N]. For the purpose of open
   access, the author has applied a CC BY public copyright license to any
   Author Accepted Manuscript version arising from this submission. The
   french co-authors were supported by CNES, France and CNRS/INSU, France
   national program of planetology and heliophysics.},
Number-of-Cited-References = {64},
Times-Cited = {0},
Usage-Count-Last-180-days = {2},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Icarus},
Doc-Delivery-Number = {UY2IA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000701351400008},
OA = {hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000477723100024,
Author = {Chen, Margaret W. and Lemon, Colby L. and Hecht, James and Sazykin,
   Stanislav and Wolf, Richard A. and Boyd, Alexander and Valek, Philip},
Title = {Diffuse Auroral Electron and Ion Precipitation Effects on RCM-E
   Comparisons With Satellite Data During the 17 March 2013 Storm},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-SPACE PHYSICS},
Year = {2019},
Volume = {124},
Number = {6},
Pages = {4194-4216},
Month = {JUN},
Abstract = {Effects of scattering of electrons from whistler chorus waves and of
   ions due to field line curvature on diffuse precipitating particle
   fluxes and ionospheric conductance during the large 17 March 2013 storm
   are examined using the self-consistent Rice Convection Model Equilibrium
   (RCM-E) model. Electrons are found to dominate the diffuse precipitating
   particle integrated energy flux, with large fluxes from similar to 21:00
   magnetic local time (MLT) eastward to similar to 11:00 MLT during the
   storm main phase. Simulated proton and oxygen ion precipitation due to
   field line curvature scattering is sporadic and localized, occurring
   where model magnetic field lines are significantly stretched on the
   night side at equatorial geocentric radial distances r(0) greater than
   or similar to 8 R E and/or at r(0) similar to 5.5 to 6.5 R-E from dusk
   to midnight where the partial ring current field has perturbed the
   magnetic field. The precipitating protons likewise contribute
   sporadically to the storm time Hall and Pedersen conductance in
   localized regions whereas the precipitating electrons are the dominate
   storm time contributor to enhanced Hall and Pedersen conductance at
   auroral magnetic latitudes on the night and morning side. The RCM-E
   model can reproduce general features of the Van Allen Probe/MagEIS
   observed trapped electron differential flux spectrograms over energies
   of similar to 37 to 150 keV. The simulations with a parameterized
   electron loss model also reproduce reasonably well the storm time
   Defense Meteorological Satellite Program integrated electron energy flux
   at 850 km at satellite crossings from predawn to midmorning. However,
   model-data agreement is not as good from dusk to premidnight where there
   are large uncertainties in the electron loss model.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Chen, MW (Corresponding Author), Aerosp Corp, El Segundo, CA 90245 USA.
   Chen, Margaret W.; Lemon, Colby L.; Hecht, James, Aerosp Corp, El Segundo, CA 90245 USA.
   Sazykin, Stanislav; Wolf, Richard A., Rice Univ, Dept Phys \& Astron, Houston, TX USA.
   Boyd, Alexander, New Mexico Consortium, Los Alamos, NM USA.
   Valek, Philip, Southwest Res Inst, San Antonio, TX USA.},
DOI = {10.1029/2019JA026545},
ISSN = {2169-9380},
EISSN = {2169-9402},
Keywords-Plus = {PITCH-ANGLE DIFFUSION; RADIATION BELT ELECTRONS; RING CURRENT
   SIMULATIONS; RELATIVISTIC ELECTRONS; MODEL; SHEET; ENERGY; LOSSES;
   LIFETIMES; PARTICLES},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {Margaret.W.Chen@aero.org},
Affiliations = {Aerospace Corporation - USA; Rice University; Southwest Research
   Institute},
ResearcherID-Numbers = {Chen, Margaret W/C-9658-2013
   },
ORCID-Numbers = {Chen, Margaret W/0000-0001-7771-4771
   Valek, Philip/0000-0002-2318-8750
   Boyd, Alexander/0000-0002-9725-508X
   Sazykin, Stanislav/0000-0002-9401-4248
   Lemon, Colby/0000-0002-2189-5769},
Funding-Acknowledgement = {NASA {[}NNX16AG72G, NNX14AF35G, NNX16AH46G, NNX14AE04G]; NSF {[}AGS
   1602862, AGS-1343072]; Aerospace Technical Investment Program; Princeton
   University {[}SUB0000155]; Van Allen Probes project under NASA
   {[}NAS501072]; NASA {[}NNX16AG72G, 904226, NNX14AE04G, 685424,
   NNX14AF35G, 683497, NNX16AH46G, 904184] Funding Source: Federal RePORTER},
Funding-Text = {We thank Rod Heelis at University of Texas at Dallas for providing the
   DMSP Ion Drift Meter data used in this study. We acknowledge Dave
   McComas of Princeton University for the use of the TWINS ENA data
   (available at http://twins.swri.edu).All Van Allen Probes (MagEIS) data
   used in this study are also publicly available at
   http://rbspect.lanl.gov website. The OMNI data were obtained from the
   GSFC/SPDF OMNIWeb interface at http://omniweb.gsfc.nasa.gov website. We
   thank numerous geomagnetic observatories (Kakioka, JMA, Honolulu and San
   Juan, USGS, Hermanus, RSA, and Alibag, IIG, NiCT, INTERMAGNET, and many
   others) for their cooperation in making the SYM-H index available. The
   VAP/MagEIS, DMSP, TWINS, SYM-H data, and simulation data used to make
   the figures in this study are available at the Open Science Framework
   data repository (https://osf.io/aphkj/). The research at The Aerospace
   Corporation was supported by the NASA grants NNX16AG72G, NNX14AF35G, and
   NNX16AH46G, the NSF grant AGS 1602862, the Aerospace Technical
   Investment Program, and a subcontract SUB0000155 from Princeton
   University. The work of R. A. W. and S. S. at Rice University was
   supported by the NASA grant NNX14AE04G and the NSF grant AGS-1343072.
   Research at the New Mexico Consortium was supported by the Van Allen
   Probes project under NASA prime contract NAS501072.},
Number-of-Cited-References = {85},
Times-Cited = {17},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {2},
Journal-ISO = {J. Geophys. Res-Space Phys.},
Doc-Delivery-Number = {IM1BJ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000477723100024},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000519120200007,
Author = {Hiatt, Matthew and Sonke, Willem and Addink, Elisabeth A. and van Dijk,
   Wout M. and van Kreveld, Marc and Ophelders, Tim and Verbeek, Kevin and
   Vlaming, Joyce and Speckmann, Bettina and Kleinhans, Maarten G.},
Title = {Geometry and Topology of Estuary and Braided River Channel Networks
   Automatically Extracted From Topographic Data},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE},
Year = {2020},
Volume = {125},
Number = {1},
Month = {JAN},
Abstract = {Automatic extraction of channel networks from topography in systems with
   multiple interconnected channels, like braided rivers and estuaries,
   remains a major challenge in hydrology and geomorphology. Representing
   channelized systems as networks provides a mathematical framework for
   analyzing transport and geomorphology. In this paper, we introduce a
   mathematically rigorous methodology and software for extracting channel
   network topology and geometry from digital elevation models (DEMs) and
   analyze such channel networks in estuaries and braided rivers. Channels
   are represented as network links, while channel confluences and
   bifurcations are represented as network nodes. We analyze and compare
   DEMs from the field and those generated by numerical modeling. We use a
   metric called the volume parameter that characterizes the volume of
   deposited material separating channels to quantify the volume of
   reworkable sediment deposited between links, which is a measure for the
   spatial scale associated with each network link. Scale asymmetry is
   observed in most links downstream of bifurcations, indicating geometric
   asymmetry and bifurcation stability. The length of links relative to
   system size scales with volume parameter value to the power of
   0.24-0.35, while the number of links decreases and does not exhibit
   power law behavior. Link depth distributions indicate that the estuaries
   studied tend to organize around a deep main channel that exists at the
   largest scale while braided rivers have channel depths that are more
   evenly distributed across scales. The methods and results presented
   establish a benchmark for quantifying the topology and geometry of
   multichannel networks from DEMs with a new automatic extraction tool.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Hiatt, M (Corresponding Author), Univ Utrecht, Fac Geosci, Dept Phys Geog, Utrecht, Netherlands.
   Hiatt, M (Corresponding Author), Louisiana State Univ, Coll Coast \& Environm, Dept Oceanog \& Coastal Sci, Baton Rouge, LA 70803 USA.
   Hiatt, M (Corresponding Author), Louisiana State Univ, Inst Coastal Studies, Baton Rouge, LA 70803 USA.
   Hiatt, Matthew; Addink, Elisabeth A.; van Dijk, Wout M.; Vlaming, Joyce; Kleinhans, Maarten G., Univ Utrecht, Fac Geosci, Dept Phys Geog, Utrecht, Netherlands.
   Hiatt, Matthew, Louisiana State Univ, Coll Coast \& Environm, Dept Oceanog \& Coastal Sci, Baton Rouge, LA 70803 USA.
   Hiatt, Matthew, Louisiana State Univ, Inst Coastal Studies, Baton Rouge, LA 70803 USA.
   Sonke, Willem; Verbeek, Kevin; Speckmann, Bettina, TU Eindhoven, Dept Math \& Comp Sci, Eindhoven, Netherlands.
   van Kreveld, Marc, Univ Utrecht, Dept Informat \& Comp Sci, Utrecht, Netherlands.
   Ophelders, Tim, Michigan State Univ, Dept Computat Math Sci \& Engn, E Lansing, MI 48824 USA.},
DOI = {10.1029/2019JF005206},
Article-Number = {e2019JF005206},
ISSN = {2169-9003},
EISSN = {2169-9011},
Keywords = {channel network extraction; estuaries; braided rivers; network analysis;
   estuarine geomorphology; fluvial geomorphology},
Keywords-Plus = {HIGH-RESOLUTION TOPOGRAPHY; SHOAL MARGIN COLLAPSES; SEDIMENT TRANSPORT;
   DRAINAGE DENSITY; FLOW STRUCTURE; BED RIVERS; MORPHOLOGY; DYNAMICS;
   VEGETATION; GRAVEL},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {mhiatt1@lsu.edu},
Affiliations = {Utrecht University; Louisiana State University System; Louisiana State
   University; Louisiana State University System; Louisiana State
   University; Eindhoven University of Technology; Utrecht University;
   Michigan State University},
ResearcherID-Numbers = {van Dijk, Wout M/K-9411-2013
   Kleinhans, Maarten/L-6697-2016
   Addink, Elisabeth A/E-3340-2012
   },
ORCID-Numbers = {van Dijk, Wout M/0000-0002-7276-1824
   Kleinhans, Maarten/0000-0002-9484-1673
   Addink, Elisabeth A/0000-0002-0919-6498
   Hiatt, Matthew/0000-0003-3680-2542
   van Kreveld, Marc/0000-0001-8208-3468
   Sonke, Willem/0000-0001-9553-7385},
Funding-Acknowledgement = {ERC Consolidator Grant {[}647570]; Netherlands Organisation for
   Scientific Research (NWO) {[}639.023.208, 639.021.541, 016.140.316]},
Funding-Text = {LowPath has been implemented in the software package TTGA (Topological
   Tools for Geomorphological Analysis), available as open-source software
   online (at https://github.com/tue-aga/ttgawith DOI
   https://doi.org/10.5281/zenodo.3518174). Experiments were performed with
   TTGA version 1.3.6, which has no significant functional differences to
   the currently available version 1.4.0. Input images for each data set
   are available at Hiatt (2019). Preprocessing and postprocessing scripts
   written for Matlab are available in an open-access data repository at
   https://figshare.com/articles/Exampled-Input-Files-for-Low-Path/10324529
   (Hiatt, 2019). We thank the Editor A. J. F. Hoitink, Associate Editor C.
   Ancey, reviewer C. Paola, and one anonymous reviewer for providing
   valuable comments that helped improve this manuscript. In theoretical
   computer science, it is customary to list authors in alphabetical order.
   Therefore, in the reference (Kleinhans et al., 2019), the author order
   does not reflect the contributions of the authors. M. Hiatt and M.G.
   Kleinhans were supported by an ERC Consolidator Grant (Agreement 647570)
   awarded to M. G. Kleinhans. T. Ophelders, W. Sonke, and B. Speckmann
   were supported by the Netherlands Organisation for Scientific Research
   (NWO) under Project 639.023.208 (Vici granted to B. Speckmann), K.
   Verbeek under Project 639.021.541 (Veni granted to K. Verbeek), and W.
   M. van Dijk under project 016.140.316 (Vici granted to M. G. Kleinhans).
   Authors contributed to the following portions of the project:
   conceptualization (M. H., W. S., E. A. A., M. vK., T. O., K. V., B. S.,
   and M. G. K.), formal analysis (M. H., W. S., W. M. vD., T.., and J.
   V.), funding acquisition (B. S. and M. G. K.), methodology (M. H., W.
   S., and W. M. vD.), software (W. S., T. O., and K. V.), supervision (B.
   S. and M. G. K.), and manuscript preparation (M. H., W. S., W. M. vD.,
   and M. G. K.).},
Number-of-Cited-References = {103},
Times-Cited = {12},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {13},
Journal-ISO = {J. Geophys. Res.-Earth Surf.},
Doc-Delivery-Number = {KT6JH},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000519120200007},
OA = {Green Submitted, hybrid, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000869025800001,
Author = {Shahriyari, Mina and Islam, Md Rezaul and Sakib, Sadman M. and Rinn,
   Malte and Rika, Anastasia and Krueger, Dennis and Kaurani, Lalit and
   Gisa, Verena and Winterhoff, Mandy and Anandakumar, Harithaa and
   Shomroni, Orr and Schmidt, Matthias and Salinas, Gabriela and Unger,
   Andreas and Linke, Wolfgang A. and Zschuentzsch, Jana and Schmidt, Jens
   and Bassel-Duby, Rhonda and Olson, Eric N. and Fischer, Andre and
   Zimmermann, Wolfram-Hubertus and Tiburcy, Malte},
Title = {Engineered skeletal muscle recapitulates human muscle development,
   regeneration and dystrophy},
Journal = {JOURNAL OF CACHEXIA SARCOPENIA AND MUSCLE},
Year = {2022},
Volume = {13},
Number = {6},
Pages = {3106-3121},
Month = {DEC},
Abstract = {Background Human pluripotent stem cell-derived muscle models show great
   potential for translational research. Here, we describe developmentally
   inspired methods for the derivation of skeletal muscle cells and their
   utility in skeletal muscle tissue engineering with the aim to model
   skeletal muscle regeneration and dystrophy in vitro.
   Methods Key steps include the directed differentiation of human
   pluripotent stem cells to embryonic muscle progenitors followed by
   primary and secondary foetal myogenesis into three-dimensional muscle.
   To simulate Duchenne muscular dystrophy (DMD), a patient-specific
   induced pluripotent stem cell line was compared to a CRISPR/Cas9-edited
   isogenic control line.
   Results The established skeletal muscle differentiation protocol
   robustly and faithfully recapitulates critical steps of embryonic
   myogenesis in two-dimensional and three-dimensional cultures, resulting
   in functional human skeletal muscle organoids (SMOs) and engineered
   skeletal muscles (ESMs) with a regeneration-competent satellite-like
   cell pool. Tissue- engineered muscle exhibits organotypic maturation and
   function (up to 5.7 +/- 0.5 mN tetanic twitch tension at 100 Hz in ESM).
   Contractile performance could be further enhanced by timed thyroid
   hormone treatment, increasing the speed of contraction (time to peak
   contraction) as well as relaxation (time to 50\% relaxation) of single
   twitches from 107 +/- 2 to 75 +/- 4 ms (P < 0.05) and from 146 +/- 6 to
   100 +/- 6 ms (P < 0.05), respectively. Satellite-like cells could be
   documented as largely quiescent PAX7+ cells (75 +/- 6\% Ki67-) located
   adjacent to muscle fibres confined under a laminin-containing basal
   membrane. Activation of the engineered satellite-like cell niche was
   documented in a cardiotoxin injury model with marked recovery of
   contractility to 57 +/- 8\% of the pre-injury force 21 days post-injury
   (P < 0.05 compared to Day 2 post-injury), which was completely blocked
   by preceding irradiation. Absence of dystrophin in DMD ESM caused a
   marked reduction of contractile force (-35 +/- 7\%, P < 0.05) and
   impaired expression of fast myosin isoforms resulting in prolonged
   contraction (175 +/- 14 ms, P < 0.05 vs. gene-edited control) and
   relaxation (238 +/- 22 ms, P < 0.05 vs. gene-edited control) times.
   Restoration of dystrophin levels by gene editing rescued the DMD
   phenotype in ESM.
   Conclusions We introduce human muscle models with canonical properties
   of bona fide skeletal muscle in vivo to study muscle development,
   maturation, disease and repair.},
Publisher = {WILEY},
Address = {111 RIVER ST, HOBOKEN 07030-5774, NJ USA},
Type = {Article},
Language = {English},
Affiliation = {Zimmermann, WH; Tiburcy, M (Corresponding Author), Georg August Univ, Univ Med Ctr Gottingen, Inst Pharmacol \& Toxicol, Robert Koch Str 40, D-37075 Gottingen, Germany.
   Shahriyari, Mina; Rinn, Malte; Rika, Anastasia; Winterhoff, Mandy; Anandakumar, Harithaa; Zimmermann, Wolfram-Hubertus; Tiburcy, Malte, Georg August Univ, Univ Med Ctr Gottingen, Inst Pharmacol \& Toxicol, Robert Koch Str 40, D-37075 Gottingen, Germany.
   Shahriyari, Mina; Rinn, Malte; Rika, Anastasia; Winterhoff, Mandy; Anandakumar, Harithaa; Zimmermann, Wolfram-Hubertus; Tiburcy, Malte, DZHK German Ctr Cardiovasc Res, Partner Site Gottingen, Gottingen, Germany.
   Islam, Md Rezaul; Sakib, Sadman M.; Krueger, Dennis; Kaurani, Lalit; Gisa, Verena; Fischer, Andre, German Ctr Neurodegenerat Dis DZNE Gottingen, Dept Epigenet \& Syst Med Neurodegenerat Dis, Gottingen, Germany.
   Shomroni, Orr; Salinas, Gabriela, Georg August Univ, Univ Med Ctr Gottingen, Inst Human Genet, NGS Integrat Genom Core Unit, Gottingen, Germany.
   Schmidt, Matthias; Zschuentzsch, Jana; Schmidt, Jens, Georg August Univ, Univ Med Ctr Gottingen, Neuromuscular Ctr, Dept Neurol, Gottingen, Germany.
   Unger, Andreas; Linke, Wolfgang A., Univ Munster, Inst Physiol 2, Munster, Germany.
   Schmidt, Jens, Univ Hosp Brandenburg Med Sch Theodor Fontane, Dept Neurol \& Pain Treatment, Immanuel Klin Rudersdorf, Rudersdorf, Germany.
   Schmidt, Jens, Brandenburg Med Sch Theodor Fontane, Fac Hlth Sci Brandenburg, Rudersdorf, Germany.
   Bassel-Duby, Rhonda; Olson, Eric N., Univ Texas Southwestern Med Ctr Dallas, Dept Mol Biol, Dallas, TX 75390 USA.
   Bassel-Duby, Rhonda; Olson, Eric N., Univ Texas Southwestern Med Ctr Dallas, Senator Paul D Wellstone Muscular Dystrophy Coope, Dallas, TX 75390 USA.
   Bassel-Duby, Rhonda; Olson, Eric N., Univ Texas Southwestern Med Ctr Dallas, Hamon Ctr Regenerat Sci \& Med, Dallas, TX 75390 USA.
   Fischer, Andre; Zimmermann, Wolfram-Hubertus, Univ Gottingen, Cluster Excellence Multiscale Bioimaging Mol Mach, Gottingen, Germany.
   Zimmermann, Wolfram-Hubertus, Fraunhofer Inst Translat Med \& Pharmacol ITMP, Gottingen, Germany.},
DOI = {10.1002/jcsm.13094},
EarlyAccessDate = {OCT 2022},
ISSN = {2190-5991},
EISSN = {2190-6009},
Keywords = {Duchenne muscular dystrophy; hypaxial dermomyotome; limb muscle;
   satellite cells; skeletal muscle organoid; somite tissue engineering},
Keywords-Plus = {PLURIPOTENT STEM-CELLS; FIBERS; MODEL; PURIFICATION; PROGENITORS;
   GENERATION; DERIVATION; EXPANSION},
Research-Areas = {Geriatrics \& Gerontology; General \& Internal Medicine},
Web-of-Science-Categories  = {Geriatrics \& Gerontology; Medicine, General \& Internal},
Author-Email = {w.zimmermann@med.uni-goettingen.de
   m.tiburcy@med.uni-goettingen.de},
Affiliations = {University of Gottingen; German Centre for Cardiovascular Research;
   Helmholtz Association; German Center for Neurodegenerative Diseases
   (DZNE); University of Gottingen; University of Gottingen; University of
   Munster; University of Texas System; University of Texas Southwestern
   Medical Center Dallas; University of Texas System; University of Texas
   Southwestern Medical Center Dallas; University of Texas System;
   University of Texas Southwestern Medical Center Dallas; University of
   Gottingen},
ResearcherID-Numbers = {Linke, Wolfgang A/E-8662-2012
   Bassel-Duby, Rhonda/HJP-5742-2023
   Zschüntzsch, Jana/HLH-3141-2023
   Olson, Eric N./B-4391-2013
   },
ORCID-Numbers = {Bassel-Duby, Rhonda/0000-0001-7568-410X
   Zschüntzsch, Jana/0000-0002-7062-5319
   Olson, Eric N./0000-0003-1151-8262
   Kaurani, Lalit/0000-0002-2304-6111},
Funding-Acknowledgement = {German Centre for Cardiovascular Research (Deutsches Zentrum fur
   Herz-Kreislaufforschung {[}DZHK]); German Research Foundation (Deutsche
   Forschungsgemeinschaft) {[}DFG TI 956/1-1, SFB 1002 TP C04]; DZHK
   (German Centre for Cardiovascular Research); German Federal Ministry for
   Science and Education (IndiHEART) {[}161L0250A]; German Research
   Foundation (DFG) {[}SFB 1002 C04/S01, IRTG 1816, MBExC 2067]; Fondation
   Leducq {[}20CVD04]; French Muscular Dystrophy Association (Association
   Francaise contre les Myopathies {[}AFM]) {[}20987]; NIH Common Fund
   Regenerative Medicine Program; NIH Common Fund},
Funding-Text = {M.T. is supported by the German Centre for Cardiovascular Research
   (Deutsches Zentrum fur Herz-Kreislaufforschung {[}DZHK]) and the German
   Research Foundation (Deutsche Forschungsgemeinschaft) (DFG TI 956/1-1
   and SFB 1002 TP C04). W-H.Z. is supported by the DZHK (German Centre for
   Cardiovascular Research), the German Federal Ministry for Science and
   Education (IndiHEART; 161L0250A), the German Research Foundation (DFG
   SFB 1002 C04/S01, IRTG 1816 and MBExC 2067) and the Fondation Leducq
   (20CVD04). Part of the work was supported by the French Muscular
   Dystrophy Association (Association Francaise contre les Myopathies
   {[}AFM], Project No. 20987) to J.S. J.Z. and J.S. are members of the
   European reference network for neuromuscular disorders (ERN EURO-NMD).
   We acknowledge A.K. Hell and H.M. Lorenz for providing human skeletal
   muscle samples. Expert technical assistance by Iris Iben is gratefully
   acknowledged. We acknowledge Xingbo Xu, Susanne Burkhardt and Ranjit
   Pradhan for excellent technical support of the single-nucleus sequencing
   experiments. We thank J.V. Durr for support with BioRender figures.
   Generation of the GMP line LiPSC-GR1.1 (also known as TC1133 or
   RUCDRi002-A) was supported by the NIH Common Fund Regenerative Medicine
   Program. The NIH Common Fund and the National Center for Advancing
   Translational Sciences (NCATS) are joint stewards of the LiPSC-GR1.1
   resource. The TC1133 line (Master Cell Bank Lot No. 50-001-21) was
   acquired by Repairon GmbH from the National Institute of Neurological
   Disorders and Stroke (NINDS) Human Cell and Data Repository (NHCDR) and
   processed to a GMP working cell bank (WCB). Post-production cells from
   the WBC were kindly provided by Repairon GmbH to UMG for research use.
   The authors of this manuscript certify that they comply with the ethical
   guidelines for authorship and publishing in the Journal of Cachexia,
   Sarcopenia and Muscle.<SUP>40</SUP>; Open Access funding enabled and
   organized by Projekt DEAL. WOA Institution: GEORG-AUGUST-UNIVERSITAET
   GOTTINGEN Consortia Name : Projekt DEAL},
Number-of-Cited-References = {40},
Times-Cited = {9},
Usage-Count-Last-180-days = {10},
Usage-Count-Since-2013 = {33},
Journal-ISO = {J. Cachexia Sarcopenia Muscle},
Doc-Delivery-Number = {8G1ZE},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000869025800001},
OA = {gold, Green Published},
DA = {2024-01-15},
}

@article{ WOS:000659467000012,
Author = {Jeon, Taehwan and Seo, Ki-Weon and Kim, Byeong-Hoon and Kim, Jae-Seung
   and Chen, Jianli and Wilson, Clark R.},
Title = {Sea level fingerprints and regional sea level change},
Journal = {EARTH AND PLANETARY SCIENCE LETTERS},
Year = {2021},
Volume = {567},
Month = {AUG 1},
Abstract = {At global and basin scales, sea level change estimated from Gravity
   Recovery And Climate Experiment (GRACE) gravity data (measuring mass)
   and Argo float data (measuring thermal expansion) agree well with
   satellite radar altimetry (measuring sea surface height). At regional
   scales, especially near coastlines, it is more difficult to compare
   GRACE + Argo estimates with altimetry due to limited spatial resolution
   of GRACE data, and associated signal leakage from land into oceans. Here
   we estimate ocean mass changes from GRACE data corrected for land to
   ocean signal leakage. The ocean mass estimates are compared with
   altimetry data over six selected coastal regions after considering
   steric changes and sea floor surface load deformation. The results show
   that sea level fingerprint mass change estimated using leakage-corrected
   GRACE data is in the better agreement with altimetry rates than Mascon
   estimates for these oceanic locations. (C) 2021 The Author(s). Published
   by Elsevier B.V.},
Publisher = {ELSEVIER},
Address = {RADARWEG 29, 1043 NX AMSTERDAM, NETHERLANDS},
Type = {Article},
Language = {English},
Affiliation = {Seo, KW (Corresponding Author), Seoul Natl Univ, Dept Earth Sci Educ, Seoul 08826, South Korea.
   Jeon, Taehwan; Seo, Ki-Weon; Kim, Byeong-Hoon; Kim, Jae-Seung, Seoul Natl Univ, Dept Earth Sci Educ, Seoul 08826, South Korea.
   Chen, Jianli; Wilson, Clark R., Univ Texas Austin, Ctr Space Res, Austin, TX 78759 USA.
   Wilson, Clark R., Univ Texas Austin, Jackson Sch Geosci, Dept Geol Sci, Austin, TX 78712 USA.},
DOI = {10.1016/j.epsl.2021.116985},
EarlyAccessDate = {MAY 2021},
Article-Number = {116985},
ISSN = {0012-821X},
EISSN = {1385-013X},
Keywords = {sea level fingerprints; GRACE; regional sea level budget},
Keywords-Plus = {MASS CHANGE; GRACE},
Research-Areas = {Geochemistry \& Geophysics},
Web-of-Science-Categories  = {Geochemistry \& Geophysics},
Author-Email = {seokiweon@snu.ac.kr},
Affiliations = {Seoul National University (SNU); University of Texas System; University
   of Texas Austin; University of Texas System; University of Texas Austin},
ResearcherID-Numbers = {Seo, Ki-weon/AAH-7729-2021
   },
ORCID-Numbers = {Seo, Ki-weon/0000-0001-5523-4996
   Chen, Jianli/0000-0001-5405-8441
   Kim, Byeong-Hoon/0000-0001-8128-6618
   Jeon, Taehwan/0000-0002-2985-5120
   Wilson, Clark/0000-0003-1288-3245},
Funding-Acknowledgement = {Korea Institute of Marine Science and Technology promotion(KIMST)
   research grant {[}KIMST20190361, PM20020]; National Research Foundation
   of Korea (NRF) {[}2020R1A2C2006857]; NASA {[}NNL14AA00C, 1478584,
   80NSSC20K0820]; NASA Earth Surface and Interior Program {[}NNX17AG96G,
   80NSSC20K1128]},
Funding-Text = {We thank an anonymous reviewer and Editor, Dr. Jean-Philippe Avouac.
   Their review comments were very constructive, and this manuscript was
   greatly improved from the comments. This study was supported by the
   Korea Institute of Marine Science and Technology promotion(KIMST)
   research grant (KIMST20190361; PM20020), National Research Foundation of
   Korea (NRF) grant (NO. 2020R1A2C2006857). J.C. is supported by NASA
   GRACE and GRACE Follow-On Projects (under contract NNL14AA00C, JPL
   subcontract 1478584, and grant 80NSSC20K0820), and J.C. and C.R.W. are
   supported by NASA Earth Surface and Interior Program (NNX17AG96G,
   80NSSC20K1128). CSR RL06 GRACE data sets are available at
   https://podaac.jpl.nasa.gov/dataaccess, and CSR RL06 Mascon, JPL RL06
   Mascon, and GSFC v02.4 Mascon solutions can be accessed from GRACE
   Tellus website (https://grace.jpl.nasa.gov/data/get-data).CMEMS
   altimetry data is provided from
   http://marine.copernicus.eu/services-portfolio/access-to-products, and
   CCI data is available at http://www.esa-sealevel-cci.org/products.CSIRO
   altimetry data can be downloaded at
   https://www.cmar.csiro.au/sealevel/sl\_data\_cmar.html, and JPL product,
   Gridded Sea Surface Height Anomalies Climate Data Record Version
   JPL1609, is provided from
   https://podaac-tools.jpl.nasa.gov/drive/files/allData/merged\_alt/L4.Arg
   o data sets (IPRC, JAMSTEC, and SIO) are all accessible via
   https://argo.ucsd.edu/data/argo-data-products.The GIA model of ICE6G-D
   can be downloaded from Dr. Peltier's website
   (http://www.atmosp.physics.utoronto.ca/\~{}peltier/data.php).SLF
   solution and regional sea level changes used in this study are available
   from a data repository of Open Science Framework
   (https://doi.org/10.17605/OSF.IO/CDZBJ).},
Number-of-Cited-References = {52},
Times-Cited = {11},
Usage-Count-Last-180-days = {8},
Usage-Count-Since-2013 = {56},
Journal-ISO = {Earth Planet. Sci. Lett.},
Doc-Delivery-Number = {SP1XP},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000659467000012},
OA = {hybrid},
DA = {2024-01-15},
}

@article{ WOS:000444417600012,
Author = {Jessee, M. A. Nowicki and Hamburger, M. W. and Allstadt, K. and Wald, D.
   J. and Robeson, S. M. and Tanyas, H. and Hearne, M. and Thompson, E. M.},
Title = {A Global Empirical Model for Near-Real-Time Assessment of Seismically
   Induced Landslides},
Journal = {JOURNAL OF GEOPHYSICAL RESEARCH-EARTH SURFACE},
Year = {2018},
Volume = {123},
Number = {8},
Pages = {1835-1859},
Month = {AUG},
Abstract = {Earthquake-triggered landslides are a significant hazard in seismically
   active regions, but our ability to assess the hazard they pose in
   near-real-time is limited. In this study, we present a new globally
   applicable model for seismically induced landslides based on the most
   comprehensive global data set available; we use 23 landslide inventories
   that span a range of earthquake magnitudes and climatic and tectonic
   settings. We use logistic regression to relate the presence and
   distribution of earthquake-triggered landslides with spatially
   distributed estimates of ground shaking, topographic slope, lithology,
   land cover type, and a topographic index designed to estimate
   variability in soil wetness to provide an empirical model of landslide
   distribution. We tested over 100 combinations of independent predictor
   variables to find the best fitting model, using a diverse set of
   statistical tests. Blind validation tests show that the model accurately
   estimates the distribution of available landslide inventories. The
   results indicate that the model is reliable and stable, with high
   balanced accuracy (correctly versus incorrectly classified pixels) for
   the majority of test events. A cross-validation analysis shows high
   balanced accuracy for a majority of events as well. By combining
   near-real-time estimates of ground shaking with globally available
   landslide susceptibility data, this model provides a tool to estimate
   the distribution of coseismic landslide hazard within minutes of the
   occurrence of any earthquake worldwide for which a U.S. Geological
   Survey ShakeMap is available.},
Publisher = {AMER GEOPHYSICAL UNION},
Address = {2000 FLORIDA AVE NW, WASHINGTON, DC 20009 USA},
Type = {Article},
Language = {English},
Affiliation = {Jessee, MAN (Corresponding Author), Indiana Univ, Dept Earth \& Atmospher Sci, Bloomington, IN 47405 USA.
   Jessee, M. A. Nowicki; Hamburger, M. W.; Robeson, S. M., Indiana Univ, Dept Earth \& Atmospher Sci, Bloomington, IN 47405 USA.
   Allstadt, K.; Wald, D. J.; Hearne, M.; Thompson, E. M., US Geol Survey, Golden, CO USA.
   Tanyas, H., Univ Twente, Dept Earth Syst Anal, Enschede, Netherlands.},
DOI = {10.1029/2017JF004494},
ISSN = {2169-9003},
EISSN = {2169-9011},
Keywords = {landslides; earthquakes; rapid response; hazards},
Keywords-Plus = {EARTHQUAKE-INDUCED LANDSLIDES; SPATIAL-DISTRIBUTION; RAPID RESPONSE;
   2016 KAIKOURA; NEW-ZEALAND; DATABASE; IMPACTS; CHINA},
Research-Areas = {Geology},
Web-of-Science-Categories  = {Geosciences, Multidisciplinary},
Author-Email = {manowick@iu.edu},
Affiliations = {Indiana University System; Indiana University Bloomington; United States
   Department of the Interior; United States Geological Survey; University
   of Twente},
ResearcherID-Numbers = {Thompson, Eric M/E-6895-2010
   Tanyas, Hakan/AAM-4018-2021
   Wald, David/AAD-2535-2020
   Robeson, Scott M/A-9895-2008
   },
ORCID-Numbers = {Thompson, Eric M/0000-0002-6943-4806
   Tanyas, Hakan/0000-0002-0609-2140
   Wald, David/0000-0002-1454-4514
   Robeson, Scott M/0000-0002-1558-6951
   Hamburger, Michael/0000-0001-6750-7621
   Nowicki Jessee, Martha Anna/0000-0001-8076-7647},
Funding-Acknowledgement = {USGS NEHRP {[}G14AP00047, G17AP00017]},
Funding-Text = {We would like to thank the individual authors of each study focused on
   mapping the landslides caused by individual earthquakes; this work would
   not have been possible without their willingness to communicate with us
   and share their data electronically, specifically Chong Xu, who shared a
   number of landslide inventories with us. We are grateful to Jens
   Hartmann and Nils Moosdorf for sharing their global lithology (GLiM)
   database. The members of the landslide hazards research team at the
   Geologic Hazards Science Center at the USGS in Golden, Colorado,
   specifically Jonathan Godt, Randall Jibson, and Edwin Harp, provided
   much insight regarding the modeling strategy. Jing Zhu and Laurie Baise,
   whose parallel work on liquefaction modeling has provided much guidance
   for the framework for the application of this model, and their guidance
   during conversations focusing on sampling of data and statistical
   measures is appreciated. Yinzhi Wang provided assistance with the Python
   sampling code. This research was supported by two USGS NEHRP grants:
   G14AP00047 and G17AP00017. Data used in this analysis include mapped
   landslide inventories (Tanyas et al., 2017); a subset of these landslide
   inventories is publicly available in an open access data repository from
   Schmitt et al. (2017). Mean and median elevation data at 7.5c resolution
   from GMTED topography data (Danielson \& Gesch, 2011). Slope data are
   computed from the aforementioned elevation data using GMT. Ground
   shaking estimates and moment magnitude values are from the USGS ShakeMap
   System (Worden \& Wald, 2016). Maximum slope data are from Verdin et al.
   (2007). Friction data are from Godt et al. (2008). Lithology data are
   from Hartmann and Moosdorf (2012). Compound topographic index data are
   from Moore et al. ( 1991). Aridity and potential evapotranspiration data
   are from Trabucco and Zomer (2009). Mean monthly precipitation data are
   from Hijmans et al. (2005). Global land cover data for 2009 (GlobCover)
   are from Arino et al. (2012). MODIS land cover data are from Broxton,
   Zeng, Sulla-Menashe, and Troch (2014). Global land cover share data for
   2014 are from Latham et al. (2014). MODIS percent green vegetation cover
   data are from Broxton, Zeng, Scheftic, and Troch (2014). We are grateful
   for constructive reviews by Jonathan Godt, three anonymous reviewers,
   and Editors Giovanni Coco and Bryn Hubbard that significantly
   contributed to the quality of this paper.},
Number-of-Cited-References = {82},
Times-Cited = {108},
Usage-Count-Last-180-days = {8},
Usage-Count-Since-2013 = {31},
Journal-ISO = {J. Geophys. Res.-Earth Surf.},
Doc-Delivery-Number = {GT3QG},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000444417600012},
OA = {Green Published, hybrid},
DA = {2024-01-15},
}

@article{ WOS:000392129600028,
Author = {Wheeler, Heather E. and Shah, Kaanan P. and Brenner, Jonathon and
   Garcia, Tzintzuni and Aquino-Michaels, Keston and Cox, Nancy J. and
   Nicolae, Dan L. and Im, Hae Kyung and GTEx Consortium},
Title = {Survey of the Heritability and Sparse Architecture of Gene Expression
   Traits across Human Tissues},
Journal = {PLOS GENETICS},
Year = {2016},
Volume = {12},
Number = {11},
Month = {NOV},
Abstract = {Understanding the genetic architecture of gene expression traits is key
   to elucidating the underlying mechanisms of complex traits. Here, for
   the first time, we perform a systematic survey of the heritability and
   the distribution of effect sizes across all representative tissues in
   the human body. We find that local h(2) can be relatively well
   characterized with 59\% of expressed genes showing significant h(2) (FDR
   < 0.1) in the DGN whole blood cohort. However, current sample sizes (n
   <= 922) do not allow us to compute distal h(2). Bayesian Sparse Linear
   Mixed Model (BSLMM) analysis provides strong evidence that the genetic
   contribution to local expression traits is dominated by a handful of
   genetic variants rather than by the collective contribution of a large
   number of variants each of modest size. In other words, the local
   architecture of gene expression traits is sparse rather than polygenic
   across all 40 tissues (from DGN and GTEx) examined. This result is
   confirmed by the sparsity of optimal performing gene expression
   predictors via elastic net modeling. To further explore the tissue
   context specificity, we decompose the expression traits into
   cross-tissue and tissue-specific components using a novel Orthogonal
   Tissue Decomposition (OTD) approach. Through a series of simulations we
   show that the cross-tissue and tissue-specific components are
   identifiable via OTD. Heritability and sparsity estimates of these
   derived expression phenotypes show similar characteristics to the
   original traits. Consistent properties relative to prior GTEx
   multi-tissue analysis results suggest that these traits reflect the
   expected biology. Finally, we apply this knowledge to develop prediction
   models of gene expression traits for all tissues. The prediction models,
   heritability, and prediction performance R-2 for original and decomposed
   expression phenotypes are made publicly available
   (https://github.com/hakyimlab/PrediXcan).},
Publisher = {PUBLIC LIBRARY SCIENCE},
Address = {1160 BATTERY STREET, STE 100, SAN FRANCISCO, CA 94111 USA},
Type = {Article},
Language = {English},
Affiliation = {Wheeler, HE (Corresponding Author), Loyola Univ Chicago, Dept Biol, Chicago, IL 60660 USA.
   Wheeler, HE (Corresponding Author), Loyola Univ Chicago, Dept Comp Sci, Chicago, IL 60660 USA.
   Im, HK (Corresponding Author), Univ Chicago, Dept Med, Med Genet Sect, 5841 S Maryland Ave, Chicago, IL 60637 USA.
   Wheeler, Heather E., Loyola Univ Chicago, Dept Biol, Chicago, IL 60660 USA.
   Wheeler, Heather E.; Brenner, Jonathon, Loyola Univ Chicago, Dept Comp Sci, Chicago, IL 60660 USA.
   Shah, Kaanan P.; Aquino-Michaels, Keston; Nicolae, Dan L.; Im, Hae Kyung, Univ Chicago, Dept Med, Med Genet Sect, 5841 S Maryland Ave, Chicago, IL 60637 USA.
   Garcia, Tzintzuni, Univ Chicago, Ctr Res Informat, Chicago, IL 60637 USA.
   Cox, Nancy J., Vanderbilt Univ, Div Med Genet, 221 Kirkland Hall, Nashville, TN 37235 USA.},
DOI = {10.1371/journal.pgen.1006423},
Article-Number = {e1006423},
ISSN = {1553-7404},
Keywords-Plus = {REGULARIZATION PATHS; REGULATORY VARIATION; COMPLEX TRAITS; ASSOCIATION;
   PREDICTION; VARIANTS; GENOMICS; MODEL; EQTL},
Research-Areas = {Genetics \& Heredity},
Web-of-Science-Categories  = {Genetics \& Heredity},
Author-Email = {hwheeler1@luc.edu
   haky@uchicago.edu},
Affiliations = {Loyola University Chicago; Loyola University Chicago; University of
   Chicago; University of Chicago; Vanderbilt University},
ResearcherID-Numbers = {Wheeler, Heather/I-9279-2019
   Little, R/IAN-6377-2023
   },
ORCID-Numbers = {Wheeler, Heather/0000-0003-1365-9667
   Little, R/0000-0001-6831-0177
   Davis, David/0000-0002-9323-6180
   Nicolae, Dan/0000-0002-0918-4630
   Im, Hae Kyung/0000-0003-0333-5685},
Funding-Acknowledgement = {US National Institutes of Health {[}R01MH107666, K12 CA139160, T32
   MH020065, R01 MH101820, P30 DK20595, P60 DK20595, P50 DA037844, P50
   MH094267]; Loyola University Chicago; Common Fund of the Office of the
   Director of the National Institutes of Health; NCI; NHGRI; NHLBI; NIDA;
   NIMH; NINDS; NCI Leidos Biomedical Research, Inc.; National Disease
   Research Interchange {[}10XS170]; Roswell Park Cancer Institute
   {[}10XS171]; Science Care, Inc. {[}X105172]; X105172). The Laboratory,
   Data Analysis, and Coordinating Center (LDACC) {[}HHSN268201000029C];
   Leidos Biomedical Research, Inc. {[}HHSN261200800001E]; Van Andel
   Research Institute {[}10ST1035]; University of Miami {[}DA006227];
   University of Geneva {[}MH090941, MH101814]; University of Chicago
   {[}MH090951, MH090937, MH101825, MH101820]; University of North Carolina
   Chapel Hill {[}MH090936]; North Carolina State University {[}MH101819];
   Harvard University {[}MH090948]; Stanford University {[}MH101782];
   Washington University {[}MH101810]; University of Pennsylvania
   {[}MH101822]; National Institutes of Health/National Institute of Mental
   Health {[}5RC2MH089916]; National Heart, Lung, and Blood Institute
   (NHLBI); Boston University {[}NO1-HC-25195, HHSN2682015000011]; NHLBI
   {[}N02-HL-64278]; Illumina and Boston University; Intramural NHLBI
   funds; Open Science Data Cloud (OSDC) which is an Open Cloud Consortium
   (OCC)-sponsored project; Gordon and Betty Moore Foundation; National
   Science Foundation;  {[}3R01MH090941]},
Funding-Text = {We acknowledge the following US National Institutes of Health grants:
   R01MH107666 (HKI), K12 CA139160 (HKI), T32 MH020065 (KPS), R01 MH101820
   (GTEx), P30 DK20595 and P60 DK20595 (Diabetes Research and Training
   Center), P50 DA037844 (Rat Genomics), P50 MH094267 (Conte). HEW was
   supported in part by start-up funds from Loyola University Chicago. GTEx
   data: The Genotype-Tissue Expression (GTEx) Project was supported by the
   Common Fund of the Office of the Director of the National Institutes of
   Health (commonfund.nih.gov/GTEx). Additional funds were provided by the
   NCI, NHGRI, NHLBI, NIDA, NIMH, and NINDS. Donors were enrolled at
   Biospecimen Source Sites funded by NCI Leidos Biomedical Research, Inc.
   subcontracts to the National Disease Research Interchange (10XS170),
   Roswell Park Cancer Institute (10XS171), and Science Care, Inc.
   (X105172). The Laboratory, Data Analysis, and Coordinating Center
   (LDACC) was funded through a contract (HHSN268201000029C) to The Broad
   Institute, Inc. Biorepository operations were funded through a Leidos
   Biomedical Research, Inc. subcontract to Van Andel Research Institute
   (10ST1035). Additional data repository and project management were
   provided by Leidos Biomedical Research, Inc. (HHSN261200800001E). The
   Brain Bank was supported by supplements to University of Miami grant
   DA006227. Statistical Methods development grants were made to the
   University of Geneva (MH090941 \& MH101814), the University of Chicago
   (MH090951,MH090937, MH101825, \& MH101820), the University of North
   Carolina Chapel Hill (MH090936), North Carolina State University
   (MH101819), Harvard University (MH090948), Stanford University
   (MH101782), Washington University (MH101810), and to the University of
   Pennsylvania (MH101822). The datasets used for the analyses described in
   this manuscript were obtained from dbGaP at http://ncbi.nlm.nih.gov/gap
   through dbGaP accession number phs000424.v3.p1. DGN data: NIMH Study 88:
   Data was provided by Dr. Douglas F. Levinson. We gratefully acknowledge
   the resources were supported by National Institutes of Health/National
   Institute of Mental Health grants 5RC2MH089916 (PI: Douglas F. Levinson,
   M.D.; Coinvestigators: Myrna M. Weissman, Ph.D., James B. Potash, M.D.,
   MPH, Daphne Koller, Ph.D., and Alexander E. Urban, Ph.D.) and
   3R01MH090941 (Co-investigator: Daphne Koller, Ph.D.). Framingham data:
   The Framingham Heart Study is conducted and supported by the National
   Heart, Lung, and Blood Institute (NHLBI) in collaboration with Boston
   University (Contract No. NO1-HC-25195 and HHSN2682015000011). This
   manuscript was not prepared in collaboration with investigators of the
   Framingham Heart Study and does not necessarily reflect the opinions or
   views of the Framingham Heart Study, Boston University, or NHLBI.
   Funding for SHARe Affymetrix genotyping was provided by NHLBI Contract
   N02-HL-64278. SHARe Illumina genotyping was provided under an agreement
   between Illumina and Boston University. Funding for Affymetrix
   genotyping of the FHS Omni cohorts was provided by Intramural NHLBI
   funds from Andrew D. Johnson and Christopher J. O'Donnell. Additional
   funding for SABRe was provided by Division of Intramural Research,
   NHLBI, and Center for Population Studies, NHLBI. The following datasets
   were downloaded from dbGaP: phs000363.v12.p9 and phs000342.v13.p9. OSDC:
   This work made use of the Open Science Data Cloud (OSDC) which is an
   Open Cloud Consortium (OCC)-sponsored project.; This work was supported
   in part by grants from Gordon and Betty Moore Foundation and the
   National Science Foundation and major contributions from OCC members
   like the University of Chicago. Bionim bus: This work made use of the
   Bionimbus Protected Data Cloud (PDC), which is a collaboration between
   the Open Science Data Cloud (OSDC) and the IGSB (IGSB), the Center for
   Research Informatics (CRI), the Institute for Translational Medicine
   (ITM), and the University of Chicago Comprehensive Cancer Center
   (UCCCC). The Bionimbus PDC is part of the OSDC ecosystem and is funded
   as a pilot project by the NIH
   (https://www.bionimbus-pdc.opensciencedatacloud.org). The funders had no
   role in study design, data collection and analysis, decision to publish,
   or preparation of the manuscript.},
Number-of-Cited-References = {54},
Times-Cited = {86},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {19},
Journal-ISO = {PLoS Genet.},
Doc-Delivery-Number = {EH9ZA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000392129600028},
OA = {Green Published, gold},
DA = {2024-01-15},
}

@article{ WOS:000981253100001,
Author = {Kong, Ru and Tan, Yan Rui and Wulan, Naren and Ooi, Leon Qi Rong and
   Farahibozorg, Seyedeh-Rezvan and Harrison, Samuel and Bijsterbosch,
   Janine D. and Bernhardt, Boris C. and Eickhoff, Simon and Yeo, B. T.
   Thomas},
Title = {Comparison between gradients and parcellations for functional
   connectivity prediction of behavior},
Journal = {NEUROIMAGE},
Year = {2023},
Volume = {273},
Month = {JUN},
Abstract = {Resting-state functional connectivity (RSFC) is widely used to predict
   behavioral measures. To predict behavioral measures, representing RSFC
   with parcellations and gradients are the two most popular approaches.
   Here, we compare parcellation and gradient approaches for RSFC-based
   prediction of a broad range of behavioral measures in the Human
   Connectome Project (HCP) and Adolescent Brain Cognitive Development
   (ABCD) datasets. Among the parcellation approaches, we consider
   group-average ``hard `` parcellations (Schaefer et al., 2018),
   individual-specific ``hard `` parcellations (Kong et al., 2021a), and an
   individual-specific ``soft `` parcellation (spatial independent
   component analysis with dual regression; Beckmann et al., 2009). For
   gradient approaches, we consider the well-known principal gradients
   (Margulies et al., 2016) and the local gradient approach that detects
   local RSFC changes (Laumann et al., 2015). Across two regression
   algorithms, individual-specific hard-parcellation performs the best in
   the HCP dataset, while the principal gradients, spatial independent
   component analysis and group-average ``hard `` parcellations exhibit
   similar performance. On the other hand, principal gradients and all
   parcellation approaches perform similarly in the ABCD dataset. Across
   both datasets, local gradients perform the worst. Finally, we find that
   the principal gradient approach requires at least 40 to 60 gradients to
   perform as well as parcellation approaches. While most principal
   gradient studies utilize a single gradient, our results suggest that
   incorporating higher order gradients can provide significant
   behaviorally relevant information. Future work will consider the
   inclusion of additional parcellation and gradient approaches for
   comparison.},
Publisher = {ACADEMIC PRESS INC ELSEVIER SCIENCE},
Address = {525 B ST, STE 1900, SAN DIEGO, CA 92101-4495 USA},
Type = {Article},
Language = {English},
Affiliation = {Yeo, BTT (Corresponding Author), Natl Univ Singapore, CSC, TMR, ECE,1 \& WisDM, Singapore, Singapore.
   Kong, Ru; Wulan, Naren; Ooi, Leon Qi Rong; Yeo, B. T. Thomas, Natl Univ Singapore, Ctr Sleep \& Cognit CSC, Yong Loo Lin Sch Med, Singapore, Singapore.
   Kong, Ru; Wulan, Naren; Ooi, Leon Qi Rong; Yeo, B. T. Thomas, Natl Univ Singapore, Ctr Translat Magnet Resonance Res TMR, Yong Loo Lin Sch Med, Singapore, Singapore.
   Kong, Ru; Tan, Yan Rui; Wulan, Naren; Ooi, Leon Qi Rong; Yeo, B. T. Thomas, Natl Univ Singapore, Dept Elect \& Comp Engn, Singapore, Singapore.
   Kong, Ru; Wulan, Naren; Ooi, Leon Qi Rong; Yeo, B. T. Thomas, Natl Univ Singapore, Inst Hlth 1, Singapore, Singapore.
   Kong, Ru; Wulan, Naren; Ooi, Leon Qi Rong; Yeo, B. T. Thomas, Natl Univ Singapore, Inst Digital Med WisDM, Singapore, Singapore.
   Kong, Ru; Wulan, Naren; Ooi, Leon Qi Rong; Yeo, B. T. Thomas, Natl Univ Singapore, Integrat Sci \& Engn Programme ISEP, Singapore, Singapore.
   Farahibozorg, Seyedeh-Rezvan; Harrison, Samuel, Univ Oxford, Wellcome Ctr Integrat Neuroimaging, Nuffield Dept Clin Neurosci, FMRIB, Oxford, England.
   Bijsterbosch, Janine D., Washington Univ, Dept Radiol, Sch Med, St Louis, MO USA.
   Bernhardt, Boris C., McGill Univ, Montreal Neurol Inst \& Hosp, McConnell Brain Imaging Ctr, Montreal, PQ, Canada.
   Eickhoff, Simon, Heinrich Heine Univ Dusseldorf, Inst Syst Neurosci, Med Fac, Dusseldorf, Germany.
   Eickhoff, Simon, Res Ctr Julich, Inst Neurosci \& Med, Brain \& Behav INM 7, Julich, Germany.
   Yeo, B. T. Thomas, Massachusetts Gen Hosp, Martinos Ctr Biomed Imaging, Charlestown, MA USA.
   Yeo, B. T. Thomas, Natl Univ Singapore, CSC, TMR, ECE,1 \& WisDM, Singapore, Singapore.},
DOI = {10.1016/j.neuroimage.2023.120044},
EarlyAccessDate = {APR 2023},
Article-Number = {120044},
ISSN = {1053-8119},
EISSN = {1095-9572},
Keywords-Plus = {RESTING-STATE FMRI; AREAL ORGANIZATION; BRAIN; NETWORK; CORTEX; MODE;
   LINKS},
Research-Areas = {Neurosciences \& Neurology; Radiology, Nuclear Medicine \& Medical
   Imaging},
Web-of-Science-Categories  = {Neurosciences; Neuroimaging; Radiology, Nuclear Medicine \& Medical
   Imaging},
Author-Email = {thomas.yeo@nus.edu.sg},
Affiliations = {National University of Singapore; National University of Singapore;
   National University of Singapore; National University of Singapore;
   National University of Singapore; National University of Singapore;
   University of Oxford; Washington University (WUSTL); McGill University;
   Heinrich Heine University Dusseldorf; Helmholtz Association; Research
   Center Julich; Harvard University; Massachusetts General Hospital;
   National University of Singapore},
ResearcherID-Numbers = {Yeo, Thomas/X-2860-2019
   Bijsterbosch, Janine/G-7726-2018
   },
ORCID-Numbers = {Yeo, Thomas/0000-0002-0119-3276
   Bijsterbosch, Janine/0000-0002-1385-9178
   Harrison, Sam/0000-0002-5886-2389},
Funding-Acknowledgement = {Singapore National Medical Research Council (NMRC) LCG
   {[}OFLCG19May-0035]; NMRC STaR {[}STaR20nov-0003]; Singapore Ministry of
   Health (MOH) {[}CG21APR1009]; United States National Institutes of
   Health {[}R01MH120080]; Wellcome center; Wellcome Trust
   {[}203139/Z/16/Z]; Human Connectome Project, WU-Minn Consortium
   {[}1U54MH091657]; NIH Institutes and Centers; Singapore National
   Research Foundation (NRF) Fellowship; NIH Blueprint for Neuroscience
   Research; NUS Yong Loo Lin School of Medicine; Singapore National
   Medical Research Council (NMRC) LCG; NMRC STaR; Singapore Ministry of
   Health (MOH) center Grant {[}NUHSRO/2020/124/TMR/LOA]; US National
   Institutes of Health {[}OFLCG19May-0035]; the Wellcome Trust
   {[}STaR20nov-0003]; NIH Blueprint for Neuroscience Research
   {[}CG21APR1009]; National Institutes of Health {[}R01MH120080,
   U01DA041048, U01DA050989, U01DA051016, U01DA041022, U01DA051018,
   U01DA051037, U01DA050987, U01DA041174, U01DA041106, U01DA041025,
   U01DA041120];  {[}U01DA041117];  {[}U01DA041028];  {[}U01DA041134]; 
   {[}U01DA050988];  {[}U01DA051039];  {[}U01DA041156]},
Funding-Text = {Our research is supported by the Singapore National Research Foundation
   (NRF) Fellowship (Class of 2017) , the NUS Yong Loo Lin School of
   Medicine (NUHSRO/2020/124/TMR/LOA) , the Singapore National Medical
   Research Council (NMRC) LCG (OFLCG19May-0035) , NMRC STaR
   (STaR20nov-0003) , Singapore Ministry of Health (MOH) center Grant
   (CG21APR1009) and the United States National Institutes of Health
   (R01MH120080) . Our computational work was partially performed on
   resources of the National Supercomputing center, Singapore (https://
   www.nscc.sg) . Any opinions, findings and conclusions or recommendations
   expressed in this material are those of the authors and do not reflect
   the views of the Singapore NRF, NMRC or MOH. The Wellcome center for
   Integrative Neuroimaging is supported by core funding from the Wellcome
   Trust (203139/Z/16/Z) . For the pur-pose of open access, the author has
   applied a CC BY public copyright license to any Author Accepted
   Manuscript version arising from this submission. Data were provided
   {[}in part] by the Human Connectome Project, WU-Minn Consortium
   (Principal Investigators: David Van Essen and Kamil Ugurbil;
   1U54MH091657) funded by the 16 NIH Institutes and Centers that support
   the NIH Blueprint for Neuroscience Research; and by the McDonnell Center
   for Systems Neuroscience at Washington Uni- versity. Data used in the
   preparation of this article were obtained from the Adolescent Brain
   Cognitive DevelopmentSM (ABCD) Study (https://abcdstudy.org) , held in
   the NIMH Data Archive (NDA) . This is a multisite, longitudinal study
   designed to recruit more than 10,000 children age 9-10 and follow them
   over 10 years into early adulthood. The ABCD Study is supported by the
   National Institutes of Health and additional federal partners under
   award numbers U01DA041048, U01DA050989, U01DA051016, U01DA041022,
   U01DA051018, U01DA051037, U01DA050987, U01DA041174, U01DA041106,
   U01DA041117, U01DA041028, U01DA041134, U01DA050988, U01DA051039,
   U01DA041156, U01DA041025, U01DA041120, U01DA051038, U01DA041148,
   U01DA041093, U01DA041089, U24DA041123, U24DA041147. A full list of
   supporters is available at https://abcdstudy.org/federal-partners.html.
   A listing of participating sites and a complete listing of the study
   investigators can be found at
   https://abcdstudy.org/consortium\_members/. ABCD consortium inves-
   tigators designed and implemented the study and/or provided data but did
   not necessarily participate in the analysis or writing of this report.
   This manuscript reflects the views of the authors and may not reflect
   the opinions or views of the NIH or ABCD consortium investigators. The
   ABCD data repository grows and changes over time. The ABCD data used in
   this report came from http://dx.doi.org/10.15154/1504041.},
Number-of-Cited-References = {74},
Times-Cited = {1},
Usage-Count-Last-180-days = {5},
Usage-Count-Since-2013 = {6},
Journal-ISO = {Neuroimage},
Doc-Delivery-Number = {F3GC9},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000981253100001},
OA = {Green Published, Green Submitted, Green Accepted, gold},
DA = {2024-01-15},
}

@article{ WOS:000372152400015,
Author = {Stacey, Simon N. and Kehr, Birte and Gudmundsson, Julius and Zink,
   Florian and Jonasdottir, Aslaug and Gudjonsson, Sigurjon A. and
   Sigurdsson, Asgeir and Halldorsson, Bjarni V. and Agnarsson, Bjarni A.
   and Benediktsdottir, Kristrun R. and Aben, Katja K. H. and Vermeulen,
   Sitah H. and Cremers, Ruben G. and Panadero, Angeles and Helfand, Brian
   T. and Cooper, Phillip R. and Donovan, Jenny L. and Hamdy, Freddie C.
   and Jinga, Viorel and Okamoto, Ichiro and Jonasson, Jon G. and
   Tryggvadottir, Laufey and Johannsdottir, Hrefna and Kristinsdottir, Anna
   M. and Masson, Gisli and Magnusson, Olafur T. and Iordache, Paul D. and
   Helgason, Agnar and Helgason, Hannes and Sulem, Patrick and
   Gudbjartsson, Daniel F. and Kong, Augustine and Jonsson, Eirikur and
   Barkardottir, Rosa B. and Einarsson, Gudmundur V. and Rafnar, Thorunn
   and Thorsteinsdottir, Unnur and Mates, Ioan N. and Neal, David E. and
   Catalona, William J. and Mayordomo, Jose I. and Kiemeney, Lambertus A.
   and Thorleifsson, Gudmar and Stefansson, Kari},
Title = {Insertion of an SVA-E retrotransposon into the <i>CASP8</i> gene is
   associated with protection against prostate cancer},
Journal = {HUMAN MOLECULAR GENETICS},
Year = {2016},
Volume = {25},
Number = {5},
Pages = {1008-1018},
Month = {MAR 1},
Abstract = {Transcriptional and splicing anomalies have been observed in intron 8 of
   the CASP8 gene (encoding procaspase-8) in association with cutaneous
   basal-cell carcinoma (BCC) and linked to a germline SNP rs700635. Here,
   we show that the rs700635{[}C] allele, which is associated with
   increased risk of BCC and breast cancer, is protective against prostate
   cancer {[}odds ratio (OR) = 0.91, P = 1.0 x 10(-6)]. rs700635{[}C] is
   also associated with failures to correctly splice out CASP8 intron 8 in
   breast and prostate tumours and in corresponding normal tissues.
   Investigation of rs700635{[}C] carriers revealed that they have a
   human-specific short interspersed element-variable number of tandem
   repeat-Alu (SINE-VNTR-Alu), subfamily-E retrotransposon (SVA-E) inserted
   into CASP8 intron 8. The SVA-E shows evidence of prior activity, because
   it has transduced some CASP8 sequences during subsequent
   retrotransposition events. Whole-genome sequence (WGS) data were used to
   tag the SVA-E with a surrogate SNP rs1035142{[}T] (r(2) = 0.999), which
   showed associations with both the splicing anomalies (P = 6.5 x 10(-32))
   and with protection against prostate cancer (OR = 0.91, P = 3.8 x
   10(-7)).},
Publisher = {OXFORD UNIV PRESS},
Address = {GREAT CLARENDON ST, OXFORD OX2 6DP, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Stacey, SN; Stefansson, K (Corresponding Author), deCODE Genet, Sturlugata 8, IS-101 Reykjavik, Iceland.
   Stacey, Simon N.; Kehr, Birte; Gudmundsson, Julius; Zink, Florian; Jonasdottir, Aslaug; Gudjonsson, Sigurjon A.; Sigurdsson, Asgeir; Halldorsson, Bjarni V.; Johannsdottir, Hrefna; Kristinsdottir, Anna M.; Masson, Gisli; Magnusson, Olafur T.; Helgason, Agnar; Helgason, Hannes; Sulem, Patrick; Gudbjartsson, Daniel F.; Kong, Augustine; Rafnar, Thorunn; Thorsteinsdottir, Unnur; Thorleifsson, Gudmar; Stefansson, Kari, deCODE Genet AMGEN, Sturlugata 8, IS-101 Reykjavik, Iceland.
   Halldorsson, Bjarni V.; Iordache, Paul D., Reykjavik Univ, Sch Sci \& Engn, Inst Biomed \& Neural Engn, IS-101 Reykjavik, Iceland.
   Agnarsson, Bjarni A.; Benediktsdottir, Kristrun R.; Jonasson, Jon G.; Jonsson, Eirikur; Barkardottir, Rosa B.; Einarsson, Gudmundur V., Landspitali Univ Hosp, IS-101 Reykjavik, Iceland.
   Agnarsson, Bjarni A.; Benediktsdottir, Kristrun R.; Jonasson, Jon G.; Jonsson, Eirikur; Barkardottir, Rosa B.; Einarsson, Gudmundur V.; Thorsteinsdottir, Unnur; Stefansson, Kari, Univ Iceland, Fac Med, IS-101 Reykjavik, Iceland.
   Helgason, Agnar, Univ Iceland, Dept Anthropol, IS-101 Reykjavik, Iceland.
   Helgason, Hannes; Gudbjartsson, Daniel F., Univ Iceland, Sch Engn \& Nat Sci, IS-101 Reykjavik, Iceland.
   Aben, Katja K. H., Netherlands Comprehens Canc Org, NL-3501 GD Utrecht, Netherlands.
   Aben, Katja K. H.; Vermeulen, Sitah H.; Cremers, Ruben G.; Kiemeney, Lambertus A., Radboud Univ Nijmegen, Med Ctr, Radboud Inst Hlth Sci, NL-6500 HB Nijmegen, Netherlands.
   Panadero, Angeles, Ciudad Coria Hosp, Div Med Oncol, Coria 10800, Spain.
   Helfand, Brian T., NorthShore Univ Hlth Syst, Div Urol, Evanston, IL 60201 USA.
   Cooper, Phillip R.; Catalona, William J., Northwestern Univ, Feinberg Sch Med, Dept Urol, Chicago, IL 60611 USA.
   Donovan, Jenny L., Univ Bristol, Sch Social \& Community Med, Bristol BS8 1TH, Avon, England.
   Hamdy, Freddie C.; Neal, David E., Univ Oxford, John Radcliffe Hosp, Nuffield Dept Surg Sci, Oxford OX3 9DU, England.
   Jinga, Viorel, Univ Med \& Pharm Carol Davila, Theodore Burghele Urol Clin, Str Dionisie Lupu 37, Bucharest 020021, Romania.
   Okamoto, Ichiro, Med Univ Vienna, Dept Dermatol, Wahringer Gutel 18-20, A-1090 Vienna, Austria.
   Jonasson, Jon G.; Tryggvadottir, Laufey, Iceland Canc Registry, Skogarhlid 8, IS-105 Reykjavik, Iceland.
   Mates, Ioan N., Univ Med \& Pharm Carol Davila, St Mary Gen Surg Clin, Blv I Mihalache 29-43, Bucharest 011172, Romania.
   Neal, David E., Univ Cambridge, Addenbrookes Hosp, Ctr Oncol, Cambridge CB2 0QQ, England.
   Mayordomo, Jose I., Univ Colorado, Div Med Oncol, Aurora, CO 80045 USA.},
DOI = {10.1093/hmg/ddv622},
ISSN = {0964-6906},
EISSN = {1460-2083},
Keywords-Plus = {GENOME-WIDE ASSOCIATION; BASAL-CELL CARCINOMA; BREAST-CANCER;
   SUSCEPTIBILITY LOCI; REDUCED RISK; DISEASE; VARIANT; IDENTIFICATION;
   EXPRESSION; CASPASE-8},
Research-Areas = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
Web-of-Science-Categories  = {Biochemistry \& Molecular Biology; Genetics \& Heredity},
Author-Email = {simon.stacey@decode.is
   kari.stefansson@decode.is},
Affiliations = {Reykjavik University; Landspitali National University Hospital;
   University of Iceland; University of Iceland; University of Iceland;
   Radboud University Nijmegen; NorthShore University Health System;
   Northwestern University; Feinberg School of Medicine; University of
   Bristol; University of Oxford; Carol Davila University of Medicine \&
   Pharmacy; Medical University of Vienna; Carol Davila University of
   Medicine \& Pharmacy; Cambridge University Hospitals NHS Foundation
   Trust; Addenbrooke's Hospital; University of Cambridge; University of
   Colorado System; University of Colorado Anschutz Medical Campus},
ResearcherID-Numbers = {Kiemeney, Lambertus A./D-3357-2009
   Stefansson, Kari/AAE-7187-2019
   Kehr, Birte/AAU-4853-2020
   Aben, Katja KH/G-9686-2016
   Mates, Ioan Nicolae/E-9255-2017
   Helgason, Agnar/K-1522-2015
   Vermeulen, Sita H./L-4716-2015
   },
ORCID-Numbers = {Kiemeney, Lambertus A./0000-0002-2368-1326
   Kehr, Birte/0000-0002-3417-7504
   Aben, Katja KH/0000-0002-0214-2147
   Vermeulen, Sita H./0000-0003-4913-8601
   Halldorsson, Bjarni/0000-0003-0756-0767
   Kong, Augustine/0000-0001-8193-5438
   Helgason, Agnar/0000-0002-8545-3767
   Masson, Gisli/0000-0003-0493-8242
   Hamdy, Freddie/0000-0003-2627-2154
   Ioan Nicoale, Mates/0000-0001-7210-0615
   Gudjonsson, Sigurjon A./0000-0001-9314-7412
   Jonasson, Jon G./0000-0002-2635-5032},
Funding-Acknowledgement = {National Cancer Research Institute (NCRI) {[}G0500966/75466]; Department
   of Health, Medical Research Council; Cancer Research UK; University of
   Cambridge; NIHR; Department of Health; Anniversary Fund of the Austrian
   National Bank {[}15079]; Medical and Scientific Fund of the Mayor of the
   City of Vienna {[}10077]; Common Fund of the Office of the Director of
   the National Institutes of Health; NCI; NHGRI; NHLBI; NIDA; NIMH; NINDS;
   NCI\textbackslash{}SAIC-Frederick, Inc. (SAIC-F) {[}10XS170]; Roswell
   Park Cancer Institute {[}10XS171]; Science Care, Inc. {[}X10S172];
   SAIC-F {[}10ST1035, HHSN261200800001E]; deCODE genetics/AMGEN; 
   {[}HHSN268201000029C];  {[}DA006227];  {[}DA033684];  {[}N01MH000028]; 
   {[}MH090941];  {[}MH101814];  {[}MH090951];  {[}MH090937]; 
   {[}MH101820];  {[}MH101825];  {[}MH090936];  {[}MH101819]; 
   {[}MH090948];  {[}MH101782];  {[}MH101810];  {[}MH101822]; National
   Institute for Health Research {[}NF-SI-0509-10242] Funding Source:
   researchfish},
Funding-Text = {The UK arm of the study acknowledges support from the National Cancer
   Research Institute (NCRI) for the ProMPT study {[}National Institute of
   Health Research (NIHR) collaborative study grant G0500966/75466]. The
   NCRI is formed by the Department of Health, Medical Research Council and
   Cancer Research UK. The collaborations are supported by the University
   of Cambridge, Cancer Research UK and the NIHR-funded Cambridge
   Bio-medical Research Centre, Cambridge, UK. We also thank the NIHR,
   Hutchison Whampoa Limited, the Human Research Tissue Bank (Addenbrooke's
   Hospital) and Cancer Research UK. The Department of Health funded the
   ProtecT study through the NIHR Health Technology Assessment programme.
   We also acknowledge to support of the research staff in S4 who so
   carefully curated the samples and the follow-up data (Jo Burge, Marie
   Corcoran, Anne George and Sara Stearn). Professor Donovan, Professor
   Hamdy and Professor Neal are National Institute for Health Research
   (NIHR) Senior Investigators. The views and opinions expressed therein
   are those of the authors and do not necessarily reflect those of the
   Department of Health. The Austrian arm of the study acknowledges support
   from the Anniversary Fund of the Austrian National Bank (grant number
   15079) and by the Medical and Scientific Fund of the Mayor of the City
   of Vienna (grant number 10077). We are grateful to the GTEx Consortium
   for early stage sharing of RNA-seq and genotypic data. The following
   acknowledgement refers to the GTEx data: The Genotype-Tissue Expression
   (GTEx) Project was supported by the Common Fund of the Office of the
   Director of the National Institutes of Health. Additional funds were
   provided by the NCI, NHGRI, NHLBI, NIDA, NIMH and NINDS. Donors were
   enrolled at Biospecimen Source Sites funded by
   NCI\textbackslash{}SAIC-Frederick, Inc. (SAIC-F) subcontracts to the
   National Disease Research Interchange (10XS170), Roswell Park Cancer
   Institute (10XS171) and Science Care, Inc. (X10S172). The Laboratory,
   Data Analysis and Coordinating Center (LDACC) was funded through a
   contract (HHSN268201000029C) to The Broad Institute, Inc. Biorepository
   operations were funded through an SAIC-F subcontract to Van Andel
   Institute (10ST1035). Additional data repository and project management
   were provided by SAIC-F (HHSN261200800001E). The Brain Bank was
   supported by a supplements to University of Miami grants DA006227 and
   DA033684 and to contract N01MH000028. Statistical Methods development
   grants were made to the University of Geneva (MH090941 and MH101814),
   the University of Chicago (MH090951, MH090937, MH101820 and MH101825),
   the University of North Carolina - Chapel Hill (MH090936 and MH101819),
   Harvard University (MH090948), Stanford University (MH101782),
   Washington University St Louis (MH101810) and the University of
   Pennsylvania (MH101822). Funding to pay the Open Access publication
   charges for this article was provided by deCODE genetics/AMGEN.},
Number-of-Cited-References = {28},
Times-Cited = {19},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {7},
Journal-ISO = {Hum. Mol. Genet.},
Doc-Delivery-Number = {DG5XA},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000372152400015},
OA = {Green Published, hybrid, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:001031357700002,
Author = {Sebenius, Isaac and Seidlitz, Jakob and Warrier, Varun and Bethlehem,
   Richard A. I. and Alexander-Bloch, Aaron and Mallard, Travis T. and
   Garcia, Rafael Romero and Bullmore, Edward T. and Morgan, Sarah E.},
Title = {Robust estimation of cortical similarity networks from brain MRI},
Journal = {NATURE NEUROSCIENCE},
Year = {2023},
Volume = {26},
Number = {8},
Pages = {1461+},
Month = {AUG},
Abstract = {Structural similarity is a growing focus for magnetic resonance imaging
   (MRI) of connectomes. Here we propose Morphometric INverse Divergence
   (MIND), a new method to estimate within-subject similarity between
   cortical areas based on the divergence between their multivariate
   distributions of multiple MRI features. Compared to the prior approach
   of morphometric similarity networks (MSNs) on n > 11,000 scans spanning
   three human datasets and one macaque dataset, MIND networks were more
   reliable, more consistent with cortical cytoarchitectonics and symmetry
   and more correlated with tract-tracing measures of axonal connectivity.
   MIND networks derived from human T1-weighted MRI were more sensitive to
   age-related changes than MSNs or networks derived by tractography of
   diffusion-weighted MRI. Gene co-expression between cortical areas was
   more strongly coupled to MIND networks than to MSNs or tractography.
   MIND network phenotypes were also more heritable, especially edges
   between structurally differentiated areas. MIND network analysis
   provides a biologically validated lens for cortical connectomics using
   readily available MRI data.
   Sebenius et al. present Morphometric INverse Divergence (MIND), a robust
   MRI-based metric of similarity between brain areas that reflects
   biological factors that define cortical network architecture, such as
   gene expression and axonal connectivity.},
Publisher = {NATURE PORTFOLIO},
Address = {HEIDELBERGER PLATZ 3, BERLIN, 14197, GERMANY},
Type = {Article},
Language = {English},
Affiliation = {Sebenius, I (Corresponding Author), Univ Cambridge, Dept Psychiat, Cambridge, England.
   Sebenius, I (Corresponding Author), Univ Cambridge, Dept Comp Sci \& Technol, Cambridge, England.
   Sebenius, Isaac; Bethlehem, Richard A. I.; Garcia, Rafael Romero; Bullmore, Edward T.; Morgan, Sarah E., Univ Cambridge, Dept Psychiat, Cambridge, England.
   Sebenius, Isaac; Morgan, Sarah E., Univ Cambridge, Dept Comp Sci \& Technol, Cambridge, England.
   Seidlitz, Jakob; Alexander-Bloch, Aaron, Univ Penn, Dept Psychiat, Philadelphia, PA USA.
   Seidlitz, Jakob; Alexander-Bloch, Aaron, Childrens Hosp Philadelphia, Dept Child \& Adolescent Psychiat \& Behav Sci, Philadelphia, PA USA.
   Seidlitz, Jakob; Alexander-Bloch, Aaron, Childrens Hosp Philadelphia, Lifespan Brain Inst, Philadelphia, PA USA.
   Warrier, Varun; Bethlehem, Richard A. I., Univ Cambridge, Autism Res Ctr, Dept Psychiat, Cambridge, England.
   Mallard, Travis T., Harvard Med Sch, Dept Psychiat, Boston, MA USA.
   Mallard, Travis T., Massachusetts Gen Hosp, Ctr Genom Med, Psychiat \& Neurodev Genet Unit, Boston, MA USA.
   Garcia, Rafael Romero, Univ Seville, Dept Fisiol Med \& Biofis, CIBERSAM, Inst Biomed Sevilla IBiS,HUVR,CSIC,ISCIII, Barcelona, Spain.
   Morgan, Sarah E., Alan Turing Inst, London, England.},
DOI = {10.1038/s41593-023-01376-7},
EarlyAccessDate = {JUL 2023},
ISSN = {1097-6256},
EISSN = {1546-1726},
Keywords-Plus = {MORPHOMETRIC SIMILARITY; QUANTITATIVE ASSESSMENT; DIFFUSION
   TRACTOGRAPHY; CONNECTIVITY; ORGANIZATION; EXPRESSION; PRINCIPLES; CORTEX},
Research-Areas = {Neurosciences \& Neurology},
Web-of-Science-Categories  = {Neurosciences},
Author-Email = {iss31@cam.ac.uk},
Affiliations = {University of Cambridge; University of Cambridge; University of
   Pennsylvania; University of Pennsylvania; Pennsylvania Medicine;
   Childrens Hospital of Philadelphia; University of Pennsylvania;
   Pennsylvania Medicine; Childrens Hospital of Philadelphia; University of
   Cambridge; Harvard University; Harvard Medical School; Harvard
   University; Massachusetts General Hospital; Consejo Superior de
   Investigaciones Cientificas (CSIC); University of Sevilla; CSIC-JA-USE -
   Instituto de Biomedicina de Sevilla (IBIS); Instituto de Salud Carlos
   III; CIBER - Centro de Investigacion Biomedica en Red; CIBERSAM},
ResearcherID-Numbers = {Alexander-Bloch, Aaron Felix/AFB-9033-2022
   Romero Garcia, Rafael/AAT-7058-2020
   },
ORCID-Numbers = {Alexander-Bloch, Aaron Felix/0000-0001-6554-1893
   Romero Garcia, Rafael/0000-0002-5199-4573
   Seidlitz, Jakob/0000-0002-8164-7476
   Bullmore, Edward/0000-0002-8955-8283
   Sebenius, Isaac/0000-0001-9927-2150
   Morgan, Sarah/0000-0002-1261-5884
   Bethlehem, Richard A.I./0000-0002-0714-0685},
Funding-Acknowledgement = {Gates-Cambridge Scholarship; Accelerate Programme for Scientific
   Discovery; Schmidt Futures; National Institute of Mental Health (NIMH);
   NIMH; St. Catharine's College Cambridge; Autism Research Trust; EMERGIA
   Junta de Andalucia program; Plan Propio of the University of Seville;
   National Institutes of Health (NIH); National Institute for Health and
   Care Research (NIHR) Senior Investigator award {[}T32MH019112];
   Accelerate Programme for Scientific Discovery - Schmidt Futures
   {[}K08MH120564]; Alan Turing Institute, London (EPSRC ); Medical
   Research Council research infrastructure award; mental health theme of
   the NIHR Cambridge Biomedical Research Centre {[}EMERGIA20\_00139]; NIH;
   NIH Blueprint for Neuroscience Research {[}T32HG010464]; McDonnell
   Center for Systems Neuroscience at Washington University; NIHR Cambridge
   Biomedical Research Centre; NIHR Applied Research Collaboration East of
   England {[}EP/N510129/1];  {[}MR/M009041/1];  {[}U01DA041048]; 
   {[}U01DA050989];  {[}U01DA051016];  {[}U01DA041022];  {[}U01DA051018]; 
   {[}U01DA051037];  {[}U01DA050987];  {[}U01DA041174];  {[}U01DA041106]; 
   {[}U01DA041117];  {[}U01DA041028];  {[}U01DA041134];  {[}U01DA050988]; 
   {[}U01DA051039];  {[}U01DA041156];  {[}U01DA041025];  {[}U01DA041120]; 
   {[}U01DA051038];  {[}U01DA041148];  {[}U01DA041093];  {[}U01DA041089]; 
   {[}U24DA041123];  {[}U24DA041147];  {[}NIHR203312]},
Funding-Text = {I.S. was generously supported by a Gates-Cambridge Scholarship and by
   the Accelerate Programme for Scientific Discovery, funded by Schmidt
   Futures. J.S. was supported by National Institute of Mental Health
   (NIMH) grant T32MH019112. A.A.B. and J.S. were supported by NIMH grant
   K08MH120564. V.W. was supported by St. Catharine's College Cambridge.
   R.A.I.B. was supported by the Autism Research Trust. R.R.G. is funded by
   the EMERGIA Junta de Andalucia program (EMERGIA20\_00139) and the Plan
   Propio of the University of Seville. T.T.M. was supported by National
   Institutes of Health (NIH) grant T32HG010464. E.T.B. was supported by a
   National Institute for Health and Care Research (NIHR) Senior
   Investigator award. S.E.M. was supported by the Accelerate Programme for
   Scientific Discovery, funded by Schmidt Futures, and a fellowship from
   the Alan Turing Institute, London (EPSRC grant EP/N510129/1). We thank
   L. Ronan for help in processing the ABCD imaging data.Data were curated
   and analyzed using a computational facility funded by a Medical Research
   Council research infrastructure award (MR/M009041/1) to the School of
   Clinical Medicine, University of Cambridge, and supported by the mental
   health theme of the NIHR Cambridge Biomedical Research Centre. The views
   expressed are those of the authors and not necessarily those of the NIH,
   the National Health Service, the NIHR or the Department of Health and
   Social Care.Data used in the preparation of this article were obtained
   from the Adolescent Brain Cognitive Development (ABCD) study
   (https://abcdstudy.org), held in the NIMH Data Archive (NDA). This is a
   multisite, longitudinal study designed to recruit more than 10,000
   children ages 9-10?years and follow them over 10?years into early
   adulthood. The ABCD study is supported by the NIH and additional federal
   partners under award numbers U01DA041048, U01DA050989, U01DA051016,
   U01DA041022, U01DA051018, U01DA051037, U01DA050987, U01DA041174,
   U01DA041106, U01DA041117, U01DA041028, U01DA041134, U01DA050988,
   U01DA051039, U01DA041156, U01DA041025, U01DA041120, U01DA051038,
   U01DA041148, U01DA041093, U01DA041089, U24DA041123 and U24DA041147. A
   full list of supporters is available at
   https://abcdstudy.org/federal-partners.html. A listing of participating
   sites and a complete listing of the study investigators can be found at
   https://abcdstudy.org/consortium\_members/. ABCD consortium
   investigators designed and implemented the study and/or provided data
   but did not necessarily participate in the analysis or writing of this
   report. This manuscript reflects the views of the authors and may not
   reflect the opinions or views of the NIH or ABCD consortium
   investigators. The ABCD data repository grows and changes over time. The
   ABCD data used in this report came from NDA Digital Object Identifier
   https://doi.org/10.15154/1528079. DOIs can be found at
   https://doi.org/10.15154/1528079.Data were provided, in part, by the
   Human Connectome Project; the WU-Minn Consortium (principal
   investigators: David Van Essen and Kamil Ugurbil; 1U54MH091657) funded
   by the 16 NIH Institutes and Centers that support the NIH Blueprint for
   Neuroscience Research; and the McDonnell Center for Systems Neuroscience
   at Washington University.All research at the Department of Psychiatry,
   University of Cambridge, was supported by the NIHR Cambridge Biomedical
   Research Centre (NIHR203312) and the NIHR Applied Research Collaboration
   East of England. The views expressed are those of the author(s) and not
   necessarily those of the NIHR or the Department of Health and Social
   Care.; We also thank the Allen Human Brain Atlas for their valuable
   contributions to open science. For the purpose of open access, the
   authors have applied a Creative Commons Attribution (CC BY) license to
   any Author Accepted Manuscript version arising from this submission.},
Number-of-Cited-References = {88},
Times-Cited = {4},
Usage-Count-Last-180-days = {15},
Usage-Count-Since-2013 = {15},
Journal-ISO = {Nat. Neurosci.},
Doc-Delivery-Number = {O3KO7},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:001031357700002},
OA = {Green Published, Green Accepted, hybrid, Green Submitted},
DA = {2024-01-15},
}

@article{ WOS:000315422500046,
Author = {Roth, Andrew and Kyzar, Evan J. and Cachat, Jonathan and Stewart, Adam
   Michael and Green, Jeremy and Gaikwad, Siddharth and O'Leary, Timothy P.
   and Tabakoff, Boris and Brown, Richard E. and Kalueff, Allan V.},
Title = {Potential translational targets revealed by linking mouse grooming
   behavioral phenotypes to gene expression using public databases},
Journal = {PROGRESS IN NEURO-PSYCHOPHARMACOLOGY \& BIOLOGICAL PSYCHIATRY},
Year = {2013},
Volume = {40},
Pages = {312-325},
Month = {JAN 10},
Abstract = {Rodent self-grooming is an important, evolutionarily conserved behavior,
   highly sensitive to pharmacological and genetic manipulations. Mice with
   aberrant grooming phenotypes are currently used to model various human
   disorders. Therefore, it is critical to understand the biology of
   grooming behavior, and to assess its translational validity to humans.
   The present in-silico study used publicly available gene expression and
   behavioral data obtained from several inbred mouse strains in the
   open-field, light-dark box, elevated plus- and elevated zero-maze tests.
   As grooming duration differed between strains, our analysis revealed
   several candidate genes with significant correlations between gene
   expression in the brain and grooming duration. The Allen Brain Atlas,
   STRING, GoMiner and Mouse Genome Informatics databases were used to
   functionally map and analyze these candidate mouse genes against their
   human orthologs, assessing the strain ranking of their expression and
   the regional distribution of expression in the mouse brain. This allowed
   us to identify an interconnected network of candidate genes (which have
   expression levels that correlate with grooming behavior), display
   altered patterns of expression in key brain areas related to grooming,
   and underlie important functions in the brain. Collectively, our results
   demonstrate the utility of large-scale, high-throughput data-mining and
   in-silico modeling for linking genomic and behavioral data, as well as
   their potential to identify novel neural targets for complex
   neurobehavioral phenotypes, including grooming. (c) 2012 Elsevier Inc.
   All rights reserved.},
Publisher = {PERGAMON-ELSEVIER SCIENCE LTD},
Address = {THE BOULEVARD, LANGFORD LANE, KIDLINGTON, OXFORD OX5 1GB, ENGLAND},
Type = {Article},
Language = {English},
Affiliation = {Kalueff, AV (Corresponding Author), Tulane Univ, Sch Med, Dept Pharmacol, Room SL-83,1430 Tulane Ave, New Orleans, LA 70112 USA.
   Roth, Andrew; Kyzar, Evan J.; Cachat, Jonathan; Stewart, Adam Michael; Green, Jeremy; Gaikwad, Siddharth; Kalueff, Allan V., Tulane Univ, Sch Med, Dept Pharmacol \& Neurosci Program, New Orleans, LA 70112 USA.
   O'Leary, Timothy P.; Brown, Richard E., Dalhousie Univ, Dept Psychol, Halifax, NS B3H 4R2, Canada.
   Tabakoff, Boris, Univ Colorado, Sch Med, Dept Pharmacol, Aurora, CO 80045 USA.
   Kalueff, Allan V., ZENEREI Inst, Slidell, LA 70458 USA.},
DOI = {10.1016/j.pnpbp.2012.10.015},
ISSN = {0278-5846},
EISSN = {1878-4216},
Keywords = {Anxiety in mice; Behavioral domains; Gene expression and omics; Grooming
   behavior; Neurophenotypes},
Keywords-Plus = {OBSESSIVE-COMPULSIVE DISORDER; TYROSINE-PHOSPHATASE-ALPHA; RECOMBINANT
   INBRED STRAINS; MICE LACKING; EXPERIMENTAL-MODELS; LOCOMOTOR-ACTIVITY;
   PREFRONTAL CORTEX; DRUG DISCOVERY; C57BL/6J MICE; MUTANT MICE},
Research-Areas = {Neurosciences \& Neurology; Pharmacology \& Pharmacy; Psychiatry},
Web-of-Science-Categories  = {Clinical Neurology; Neurosciences; Pharmacology \& Pharmacy; Psychiatry},
Author-Email = {avkalueff@gmail.com},
Affiliations = {Tulane University; Dalhousie University; University of Colorado System;
   University of Colorado Anschutz Medical Campus},
ResearcherID-Numbers = {Kalueff, Allan/AAB-8620-2022
   Gaikwad, Siddharth/HSF-9132-2023
   Kalueff, Allan V/B-3647-2010
   Cachat, Jonathan/AAW-1165-2021
   Tabakoff, Boris/AAX-1204-2021
   },
ORCID-Numbers = {Kalueff, Allan/0000-0002-7525-1950
   Gaikwad, Siddharth/0000-0001-6437-7016
   Kalueff, Allan V/0000-0002-7525-1950
   Cachat, Jonathan/0000-0002-6504-0869
   O'Leary, Timothy/0000-0003-4304-2772
   Kyzar, Evan/0000-0002-7688-0281},
Funding-Acknowledgement = {Tulane University; Tulane Synergy; Provost's Scholarly Enrichment
   grants; ZENEREI Institute; NSERC of Canada; AstraZeneca RD Boston; NSERC},
Funding-Text = {The study was supported by Tulane University Pilot funds, Tulane Synergy
   and Provost's Scholarly Enrichment grants to AVK, as well as by ZENEREI
   Institute. The authors thank Rhian Gunn (Dalhousie University) for her
   help with this project. This study used several open-access databases,
   including the Allen Brain Atlas of gene activity in the C57BL/6J mouse
   brain (ABA, http://mouse.brain-map.org/;
   http://uri.neuinfo.org/nif/registry/nif-0000-00508); GoMiner (to
   classify genes in microarray experiments,
   http://discover.nci.nih.gov/gominer/;
   http://uri.neuinfo.org/nif/registiy/nif-0000-21181), the Gene Ontology
   (GO, used by GoMiner to provide detailed gene information,
   http://www.geneontology.org/;
   http://uri.neuinfo.org/nif/registry/nif-0000-02915); the Mouse Genome
   Informatics (MGI) database of mutant and transgenic mouse models
   (http://www.informatics.jax.org;
   http://uri.neuinfo.org/nif/registry/nif-0000-00096); the Mouse Phenome
   Database (MPD, a repository of genotypic and phenotypic data, which
   allows for genotype-phenotype association, http://www.jax.org/phenome;
   http://uri.neuinfo.org/nif/registry/nif-0000-03160); the Phenogen
   Informatics (a microarray data repository and analysis tool allowing
   users to research candidate genes,
   http://phenogen.ucdenver.edu/PhenoGen/); the Drug Related Gene Database
   (DRG, describing differences in gene expression as a function of drug
   exposure, https://confluence.crbs.ucsd. edu/display/NIF/DRG;
   http://uri.neuinfo.org/nif/registiy/nif-0000-37443) and the Search Tool
   for the Retrieval of Interacting Genes (STRING, database containing all
   known and predicted interactions between proteins in over 1000 different
   species, http://string.embl.de/;
   http://uri.neuinfo.org/nif/registry/nif-0000-03503). We also used
   Cytoscape (http://cytoscape.org;
   http://uri.neuinfo.org/nif/registry/nif-0000-30404) to visualize
   protein-protein interaction networks, and the Ontological Discovery
   Environment (ODE, http://ontologicaldiscovery.org/;
   http://uri.neuinfo.org/nif/registry/nif-0000-00517) as a freely
   accessible phenotype-centered database with integrated analysis and
   visualization tools. In addition to homepage URL, we provided the
   Uniform Resource Identifier (URI) for the databases used in this study,
   directing the user to the original source regardless of its current
   URLs. This information was given here to recognize the value and
   importance of open-source, publicly accessible scientific information
   (Cheung et al., 2009). The Protein database (Pruitt et al., 2007) and
   sequence analysis using Hum-mPLoc (Shen and Chou, 2007) were also used
   in this study to characterize cellular location of protein products of
   the selected candidate gene (Fig. 3E). Grooming data was collected with
   the help of Nicola Hoffman, Lisa Currie, Vicki Savoie and Martin
   Williamson. Behavioral data collection was funded by a grant from NSERC
   of Canada to REB. Generous funds from the AstraZeneca R\&D Boston were
   used to defray cost of mice through the Mouse Phenome Project (The
   Jackson Laboratory, Bar Harbor, ME). Behavioral equipment was purchased
   with funds from an NSERC equipment grant to REB.},
Number-of-Cited-References = {113},
Times-Cited = {9},
Usage-Count-Last-180-days = {0},
Usage-Count-Since-2013 = {20},
Journal-ISO = {Prog. Neuro-Psychopharmacol. Biol. Psychiatry},
Doc-Delivery-Number = {096RR},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000315422500046},
OA = {Green Accepted},
DA = {2024-01-15},
}

@article{ WOS:000472594000001,
Author = {Kankare, E. and Huber, M. and Smartt, S. J. and Chambers, K. and Smith,
   K. W. and McBrien, O. and Chen, T-W and Flewelling, H. and Lowe, T. and
   Magnier, E. and Schultz, A. and Waters, C. and Wainscoat, R. J. and
   Willman, M. and Wright, D. and Young, D. and Aartsen, M. G. and
   Ackermann, M. and Adams, J. and Aguilar, J. A. and Ahlers, M. and
   Ahrens, M. and Alispach, C. and Altmann, D. and Andeen, K. and Anderson,
   T. and Ansseau, I and Anton, G. and Arguelles, C. and Auffenberg, J. and
   Axani, S. and Backes, P. and Bagherpour, H. and Bai, X. and Barbano, A.
   and Barwick, S. W. and Baum, V and Bay, R. and Beatty, J. J. and Becker,
   K-H and Tjus, J. Becker and BenZvi, S. and Berley, D. and Bernardini, E.
   and Besson, D. Z. and Binder, G. and Bindig, D. and Blaufuss, E. and
   Blot, S. and Bohm, C. and Boerner, M. and Boeser, S. and Botner, O. and
   Bourbeau, E. and Bourbeau, J. and Bradascio, F. and Braun, J. and Bretz,
   H-P and Bron, S. and Brostean-Kaiser, J. and Burgman, A. and Busse, R.
   S. and Carver, T. and Chen, C. and Cheung, E. and Chirkin, D. and Clark,
   K. and Classen, L. and Collin, G. H. and Conrad, J. M. and Coppin, P.
   and Correa, P. and Cowen, D. F. and Cross, R. and Dave, P. and de Andre,
   J. P. A. M. and De Clercq, C. and DeLaunay, J. J. and Dembinski, H. and
   Deoskar, K. and De Ridder, S. and Desiati, P. and de Vries, K. D. and de
   Wasseige, G. and de With, M. and DeYoung, T. and Diaz-Velez, J. C. and
   Dujmovic, H. and Dunkman, M. and Dvorak, E. and Eberhardt, B. and
   Ehrhardt, T. and Eller, P. and Evenson, P. A. and Fahey, S. and Fazely,
   A. R. and Felde, J. and Filimonov, K. and Finley, C. and Franckowiak, A.
   and Friedman, E. and Fritz, A. and Gaisser, T. K. and Gallagher, J. and
   Ganster, E. and Garrappa, S. and Gerhardt, L. and Ghorbani, K. and
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   Stachurska, J. and Stamatikos, M. and Stanev, T. and Stasik, A. and
   Stein, R. and Stettner, J. and Steuer, A. and Stezelberger, T. and
   Stokstad, R. G. and Stossl, A. and Strotjohann, N. L. and Stuttard, T.
   and Sullivan, G. W. and Sutherland, M. and Taboada, I and Tenholt, F.
   and Ter-Antonyan, S. and Terliuk, A. and Tilav, S. and Tomankova, L. and
   Tonnis, C. and Toscano, S. and Tosi, D. and Tselengidou, M. and Tung, C.
   F. and Turcati, A. and Turcotte, R. and Turley, C. F. and Ty, B. and
   Unger, E. and Elorrieta, M. A. Unland and Usner, M. and Vandenbroucke,
   J. and Van Driessche, W. and van Eijk, D. and van Eijndhoven, N. and
   Vanheule, S. and van Santen, J. and Vraeghe, M. and Walck, C. and
   Wallace, A. and Wallraff, M. and Wandkowsky, N. and Watson, T. B. and
   Weaver, C. and Weiss, M. J. and Weldert, J. and Wendt, C. and
   Werthebach, J. and Westerhoff, S. and Whelan, B. J. and Whitehorn, N.
   and Wiebe, K. and Wiebusch, C. H. and Wille, L. and Williams, D. R. and
   Wills, L. and Wolf, M. and Wood, J. and Wood, T. R. and Woschnagg, K.
   and Wrede, G. and Xu, D. L. and Xu, X. W. and Xu, Y. and Yanez, J. P.
   and Yodh, G. and Yoshida, S. and Yuan, T. and Nordin, J. and Pan-STARRS
   and IceCube Collaboration},
Title = {Search for transient optical counterparts to high-energy IceCube
   neutrinos with Pan-STARRS1},
Journal = {ASTRONOMY \& ASTROPHYSICS},
Year = {2019},
Volume = {626},
Month = {JUN 24},
Abstract = {In order to identify the sources of the observed diffuse high-energy
   neutrino flux, it is crucial to discover their electromagnetic
   counterparts. To increase the sensitivity of detecting counterparts of
   transient or variable sources by telescopes with a limited field of
   view, IceCube began releasing alerts for single high-energy (E-v > 60
   TeV) neutrino detections with sky localisation regions of order 1
   degrees radius in 2016. We used Pan-STARRS1 to follow-up five of these
   alerts during 2016-2017 to search for any optical transients that may be
   related to the neutrinos. Typically 10-20 faint m(ip1) less than or
   similar to 22.5 mag) extragalactic transients are found within the
   Pan-STARRS1 footprints and are generally consistent with being unrelated
   field supernovae (SNe) and AGN. We looked for unusual properties of the
   detected transients, such as temporal coincidence of explosion epoch
   with the IceCube timestamp, or other peculiar light curve and physical
   properties. We found only one transient that had properties worthy of a
   specific follow-up. In the Pan-STARRS1 imaging for IceCube-160427A
   (probability to be of astrophysical origin of similar to 50\%), we found
   a SN PS16cgx, located at 10.0' from the nominal IceCube direction.
   Spectroscopic observations of PS16cgx showed that it was an H-poor SN at
   redshift z = 0.2895 +/- 0.0001. The spectra and light curve resemble
   some high-energy Type Ic SNe, raising the possibility of a jet driven SN
   with an explosion epoch temporally coincident with the neutrino
   detection. However, distinguishing Type Ia and Type Ic SNe at this
   redshift is notoriously difficult. Based on all available data we
   conclude that the transient is more likely to be a Type Ia with
   relatively weak Sin absorption and a fairly normal rest-frame r-band
   light curve. If, as predicted, there is no high-energy neutrino emission
   from Type Ia SNe, then PS16cgx must be a random coincidence, and
   unrelated to the IceCube-160427A. We find no other plausible optical
   transient for any of the five IceCube events observed down to a 5 sigma
   limiting magnitude of mip1 approximate to 22 mag, between 1 day and 25
   days after detection.},
Publisher = {EDP SCIENCES S A},
Address = {17, AVE DU HOGGAR, PA COURTABOEUF, BP 112, F-91944 LES ULIS CEDEX A,
   FRANCE},
Type = {Article},
Language = {English},
Affiliation = {Kankare, E (Corresponding Author), Queens Univ Belfast, Astrophys Res Ctr, Sch Math \& Phys, Belfast BT7 1NN, Antrim, North Ireland.
   Kankare, E (Corresponding Author), Univ Turku, Dept Phys \& Astron, Tuorla Observ, Turku 20014, Finland.
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   Kankare, E., Univ Turku, Dept Phys \& Astron, Tuorla Observ, Turku 20014, Finland.
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   Barwick, S. W.; Yodh, G., Univ Calif Irvine, Dept Phys \& Astron, Irvine, CA 92697 USA.
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   Whitehorn, N., UCLA, Dept Phys \& Astron, Los Angeles, CA 90095 USA.
   Gallagher, J., Univ Wisconsin, Dept Astron, Madison, WI 53706 USA.
   Bourbeau, J.; Braun, J.; Busse, R. S.; Chirkin, D.; Desiati, P.; Diaz-Velez, J. C.; Eberhardt, B.; Fahey, S.; Ghorbani, K.; Griffith, Z.; Halzen, F.; Hanson, K.; Hokanson-Fasig, B.; Hoshina, K.; Hussain, R.; Jero, K.; Karle, A.; Kauer, M.; Kelley, J. L.; Kheirandish, A.; Lazar, J. P.; Leonard, K.; Liu, Q. R.; Luszczak, W.; Mallot, K.; Mancina, S.; Meagher, K.; Merino, G.; Park, N.; Pizzuto, A.; Safa, I; Schneider, A.; Silva, M.; Snihur, R.; Tosi, D.; Ty, B.; Vandenbroucke, J.; van Eijk, D.; Wandkowsky, N.; Wendt, C.; Werthebach, J.; Westerhoff, S.; Wille, L.; Wood, J.; Xu, D. L.; Yuan, T., Univ Wisconsin, Dept Phys, Madison, WI 53706 USA.
   Bourbeau, J.; Braun, J.; Busse, R. S.; Chirkin, D.; Desiati, P.; Diaz-Velez, J. C.; Eberhardt, B.; Fahey, S.; Ghorbani, K.; Griffith, Z.; Halzen, F.; Hanson, K.; Hokanson-Fasig, B.; Hoshina, K.; Hussain, R.; Jero, K.; Karle, A.; Kauer, M.; Kelley, J. L.; Kheirandish, A.; Lazar, J. P.; Leonard, K.; Liu, Q. R.; Luszczak, W.; Mallot, K.; Mancina, S.; Meagher, K.; Merino, G.; Park, N.; Pizzuto, A.; Safa, I; Schneider, A.; Silva, M.; Snihur, R.; Tosi, D.; Ty, B.; Vandenbroucke, J.; van Eijk, D.; Wandkowsky, N.; Wendt, C.; Werthebach, J.; Westerhoff, S.; Wille, L.; Wood, J.; Xu, D. L.; Yuan, T., Univ Wisconsin, Wisconsin IceCube Particle Astrophys Ctr, Madison, WI 53706 USA.
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DOI = {10.1051/0004-6361/201935171},
Article-Number = {A117},
ISSN = {0004-6361},
EISSN = {1432-0746},
Keywords = {astroparticle physics; neutrinos; supernovae: general},
Keywords-Plus = {DIGITAL SKY SURVEY; GAMMA-RAY BURSTS; FOLLOW-UP; SUPERNOVA RATES; IA
   SUPERNOVAE; DATA RELEASE; LIGHT-CURVE; PAN-STARRS; SPECTROGRAPH;
   CALIBRATION},
Research-Areas = {Astronomy \& Astrophysics},
Web-of-Science-Categories  = {Astronomy \& Astrophysics},
Author-Email = {e.kankare@qub.ac.uk},
Affiliations = {Queens University Belfast; University of Turku; University of Hawaii
   System; Max Planck Society; University of Minnesota System; University
   of Minnesota Twin Cities; RWTH Aachen University; University of
   Adelaide; University of Alaska System; University of Alaska Anchorage;
   University of Texas System; University of Texas Arlington; Clark Atlanta
   University; University System of Georgia; Georgia Institute of
   Technology; University System of Georgia; Georgia Institute of
   Technology; Southern University System; Southern University \& A\&M
   College; University of California System; University of California
   Berkeley; United States Department of Energy (DOE); Lawrence Berkeley
   National Laboratory; Humboldt University of Berlin; University of
   Wurzburg; Ruhr University Bochum; Universite Libre de Bruxelles; Vrije
   Universiteit Brussel; Massachusetts Institute of Technology (MIT); Chiba
   University; Chiba University; University of Canterbury; University
   System of Maryland; University of Maryland College Park; University
   System of Ohio; Ohio State University; University System of Ohio; Ohio
   State University; University System of Ohio; Ohio State University;
   University of Copenhagen; Niels Bohr Institute; Dortmund University of
   Technology; Michigan State University; University of Alberta; University
   of Erlangen Nuremberg; Technical University of Munich; University of
   Geneva; Ghent University; University of California System; University of
   California Irvine; University of Kansas; University of California
   System; University of California Los Angeles; University of Wisconsin
   System; University of Wisconsin Madison; University of Wisconsin System;
   University of Wisconsin Madison; University of Wisconsin System;
   University of Wisconsin Madison; Johannes Gutenberg University of Mainz;
   Marquette University; University of Munster; University of Delaware;
   University of Delaware; Yale University; University of Oxford; Drexel
   University; South Dakota School Mines \& Technology; University of
   Wisconsin System; University of Rochester; Stockholm University; Oskar
   Klein Centre; Stockholm University; State University of New York (SUNY)
   System; State University of New York (SUNY) Stony Brook; Sungkyunkwan
   University (SKKU); University of Alabama System; University of Alabama
   Tuscaloosa; Pennsylvania Commonwealth System of Higher Education
   (PCSHE); Pennsylvania State University; Pennsylvania State University -
   University Park; Pennsylvania Commonwealth System of Higher Education
   (PCSHE); Pennsylvania State University; Pennsylvania State University -
   University Park; Uppsala University; University of Wuppertal; Helmholtz
   Association; Deutsches Elektronen-Synchrotron (DESY); University of
   Tokyo},
ResearcherID-Numbers = {LU, LU/JEZ-4760-2023
   Anton, Gisela/C-4840-2013
   Strotjohann, Nora Linn/GPX-7122-2022
   Beatty, James/D-9310-2011
   Chambers, Kenneth/HOH-0341-2023
   Díaz Vélez, Juan Carlos/AAD-5211-2022
   Wright, Darryl/GOV-5481-2022
   Huang, Feifei/AAX-2156-2020
   Wiebusch, Christopher H.V./G-6490-2012
   Resconi, Elisa/I-3874-2016
   Kauer, Matt/AAY-7581-2020
   Maruyama, Reina H/A-1064-2013
   lu, lu/HGA-0894-2022
   Reimann, René/AAS-8239-2020
   Sandrock, Alexander/AAT-1285-2020
   Sarkar, Subir/GPT-4902-2022
   xu, ye/GQO-8972-2022
   Young, David Reid/HKN-5543-2023
   lu, lu/HII-7530-2022
   Bernardini, Elisa/AAA-4810-2020
   Schneider, Austin/JGC-9796-2023
   Kalaczyński, Piotr/P-8189-2019
   Ahlers, Markus/V-8757-2017
   Katz, Uli F/E-1925-2013
   Sarkar, Subir/G-5978-2011
   Tjus, Julia/G-8145-2012
   Koskinen, David/G-3236-2014
   sanchez, juan/GSD-8167-2022
   Rott, Carsten/ABB-1304-2021
   Whitehorn, Nathan/HDM-8864-2022
   Satalecka, Konstancja/AAT-1309-2020
   Rea, Immacolata Carmen/AAV-4830-2021
   DeYoung, Tyce/O-6895-2019
   Williams, David/HKN-3732-2023
   Aguilar Sanchez, Juan Antonio/H-4467-2015
   },
ORCID-Numbers = {Anton, Gisela/0000-0003-2039-4724
   Beatty, James/0000-0003-0481-4952
   Chambers, Kenneth/0000-0001-6965-7789
   Díaz Vélez, Juan Carlos/0000-0002-0087-0693
   Huang, Feifei/0000-0002-6014-5928
   Wiebusch, Christopher H.V./0000-0002-6418-3008
   Resconi, Elisa/0000-0003-0705-2770
   Kauer, Matt/0000-0003-1830-9076
   Maruyama, Reina H/0000-0003-2794-512X
   Reimann, René/0000-0002-1983-8271
   Sandrock, Alexander/0000-0002-6779-1172
   Bernardini, Elisa/0000-0003-3108-1141
   Kalaczyński, Piotr/0000-0001-9278-5906
   Ahlers, Markus/0000-0003-0709-5631
   Katz, Uli F/0000-0002-7063-4418
   Sarkar, Subir/0000-0002-3542-858X
   Tjus, Julia/0000-0002-1748-7367
   Koskinen, David/0000-0002-0514-5917
   Rott, Carsten/0000-0002-6958-6033
   Whitehorn, Nathan/0000-0002-3157-0407
   Satalecka, Konstancja/0000-0002-7669-266X
   Rea, Immacolata Carmen/0000-0002-3954-7754
   DeYoung, Tyce/0000-0003-4873-3783
   Deoskar, Kunal/0000-0002-1668-2347
   Stuttard, Thomas/0000-0001-7944-279X
   Lucarelli, Francesco/0000-0002-9558-8788
   /0000-0001-7909-5812
   Bron, Stephanie/0000-0002-6305-3041
   Andeen, Karen/0000-0001-9394-0007
   Aguilar Sanchez, Juan Antonio/0000-0003-2252-9514
   Sullivan, Mark/0000-0001-9053-4820
   Franckowiak, Anna/0000-0002-5605-2219
   Plum, Matthias/0000-0001-8691-242X
   Santander, Juan Marcos/0000-0001-7297-8217
   Maris, Ioana/0000-0002-5771-1124
   Taboada, Ignacio/0000-0003-3509-3457
   Kunwar, Samridha/0000-0003-4735-6103
   Stettner, Joran/0000-0003-1042-3675
   Rhode, Wolfgang/0000-0003-2636-5000
   Kolanoski, Hermann/0000-0003-0435-2524
   De Wasseige, Gwenhael/0000-0002-1010-5100
   Chen, Chujie/0000-0002-8139-4106
   Schumacher, Lisa Johanna/0000-0001-8945-6722
   Athayde Marcondes de Andre, Joao Pedro/0000-0002-8905-1351
   Desiati, Paolo/0000-0001-9768-1858
   Mancina, Sarah/0009-0003-9879-3896
   Huennefeld, Mirco/0000-0002-2827-6522
   BenZvi, Segev/0000-0001-5537-4710
   Ganster, Erik/0000-0003-4393-6944
   Meier, Maximilian/0000-0002-9483-9450
   Schneider, Austin/0000-0002-0895-3477
   Hill, Gary/0000-0001-8881-6802
   Rongen, Martin/0000-0002-7057-1007
   Stachurska, Juliana/0000-0002-0238-5608
   Sclafani, Stephen/0000-0001-9446-1219
   de Vries, Krijn/0000-0002-9842-4068
   Eller, Philipp/0000-0001-6354-5209
   Unland Elorrieta, Martin Antonio/0000-0002-6124-3255
   Sarkar, Sourav/0000-0002-1206-4330
   De Clercq, Catherine/0000-0001-5266-7059
   Meighen-Berger, Stephan/0000-0001-6579-2000
   Stein, Robert/0000-0003-2434-0387
   LIU, QINRUI/0000-0003-3379-6423
   van Eijndhoven, Nick/0000-0001-5558-3328
   Chen, Ting-Wan/0000-0002-1066-6098
   Kankare, Erkki/0000-0001-8257-3512
   Kappes, Alexander/0000-0003-1315-3711
   Lu, Lu/0000-0003-3175-7770
   Leonard DeHolton, Kayla/0000-0002-8795-0601
   Moore, Roger/0000-0003-4160-4700
   Pizzuto, Alex/0000-0002-8466-8168
   Montaruli, Teresa/0000-0001-5014-2152
   Coppin, Paul/0000-0001-6869-1280
   Correa, Pablo/0000-0002-1158-6735
   Merino, Gonzalo/0000-0002-9540-5742
   Kang, Woosik/0000-0003-3980-3778
   Kheirandish, Ali/0000-0001-7074-0539
   Arguelles-Delgado, Carlos/0000-0003-4186-4182
   Strotjohann, Nora Linn/0000-0002-4667-6730
   Blot, Summer/0000-0003-1089-3001
   Haack, Christian/0000-0003-3932-2448
   Spiczak, Glenn/0000-0002-0030-0519
   Lauber, Frederik/0000-0001-5648-5930
   Tung, Chun Fai/0000-0001-6920-7841
   Young, David/0000-0002-1229-2499
   Meagher, Kevin/0000-0003-3967-1533
   Conrad, Janet/0000-0002-6393-0438},
Funding-Acknowledgement = {University of Hawaii; NASA's Planetary Defense Office {[}NNX14AM74G];
   Queen's University Belfast; National Aeronautics and Space
   Administration {[}NNX08AR22G]; National Science Foundation
   {[}AST-1238877]; USA - U.S. National Science Foundation-Office of Polar
   Programs; U.S. National Science Foundation-Physics Division; Wisconsin
   Alumni Research Foundation; Center for High Throughput Computing (CHTC)
   at the University of Wisconsin-Madison; Open Science Grid (OSG); Extreme
   Science and Engineering Discovery Environment (XSEDE); U.S. Department
   of Energy-National Energy Research Scientific Computing Center, Particle
   astrophysics research computing center at the University of Maryland;
   Institute for Cyber-Enabled Research at Michigan State University;
   Astroparticle physics computational facility at Marquette University;
   Belgium -Funds for Scientific Research (FRS-FNRS and FWO); FWO Odysseus
   and Big Science programmes; Belgian Federal Science Policy Office
   (Belspo); Germany -Bundesministerium fur Bildung und Forschung (BMBF);
   Deutsche Forschungsgemeinschaft (DFG); Helmholtz Alliance for
   Astroparticle Physics (HAP); Initiative and Networking Fund of the
   Helmholtz Association; Deutsches Elektronen Synchrotron (DESY); High
   Performance Computing cluster of the RWTH Aachen; Sweden - Swedish
   Research Council; Swedish Polar Research Secretariat; Swedish National
   Infrastructure for Computing (SNIC); Knut and Alice Wallenberg
   Foundation; Australia - Australian Research Council; Canada - Natural
   Sciences and Engineering Research Council of Canada; Calcul Quebec;
   Compute Ontario; Canada Foundation for Innovation; WestGrid; Compute
   Canada; Denmark - Villum Fonden; Danish National Research Foundation
   (DNRF); Carlsberg Foundation; New Zealand - Marsden Fund; Japan - Japan
   Society for Promotion of Science (JSPS); Institute for Global Prominent
   Research (IGPR) of Chiba University; Science and Technology Facilities
   Council (STFC) {[}ST/P000312/1, ST/N002520/1]; European Research Council
   under the European Union {[}291222]; Alexander von Humboldt Foundation;
   (the Public ESO Spectroscopic Survey for Transient Objects Survey) ESO
   program {[}188. D-3003]; DDT programme {[}297. D-5024]; Alfred P. Sloan
   Foundation; National Science Foundation; U.S. Department of Energy O ffi
   ce of Science; University of Arizona; Brazilian Participation Group;
   Brookhaven National Laboratory; Carnegie Mellon University; University
   of Florida; French Participation Group; German Participation Group;
   Harvard University; Instituto de Astrofisica de Canarias; Michigan
   State/Notre Dame/JINA Participation Group; Johns Hopkins University;
   Lawrence Berkeley National Laboratory; Max Planck Institute for
   Astrophysics; Max Planck Institute for Extraterrestrial Physics; New
   Mexico State University; New York University; Ohio State University;
   Pennsylvania State University; University of Portsmouth; Princeton
   University; Spanish Participation Group; University of Tokyo; University
   of Utah; Vanderbilt University; University of Virginia; University of
   Washington; Yale University;  {[}GN-2016A-DD-9]; NASA {[}NNX14AM74G,
   675328] Funding Source: Federal RePORTER},
Funding-Text = {Pan-STARRS: Pan-STARRS is supported by the University of Hawaii and the
   NASA's Planetary Defense Office under Grant No NNX14AM74G and the
   Pan-STARRS Multi-messenger science collaboration is supported by Queen's
   University Belfast. The Pan-STARRS1 Surveys (PS1) have been made
   possible through contributions of the Institute for Astronomy, the
   University of Hawaii, the Pan-STARRS Project Office, the Max-Planck
   Society and its participating institutes, the Max Planck Institute for
   Astronomy, Heidelberg and the Max Planck Institute for Extraterrestrial
   Physics, Garching, The Johns Hopkins University, Durham University, the
   University of Edinburgh, Queen's University Belfast, the
   Harvard-Smithsonian Center for Astro-physics, the Las Cumbres
   Observatory Global Telescope Network Incorporated, the National Central
   University of Taiwan, the Space Telescope Science Institute, the
   National Aeronautics and Space Administration under Grant No. NNX08AR22G
   issued through the Planetary Science Division of the NASA Science
   Mission Directorate, the National Science Foundation under Grant No.
   AST-1238877, the University of Maryland, and Eotvos Lorand University
   (ELTE). IceCube: The IceCube collaboration acknowledges the significant
   contributions to this manuscript from Anna Franckowiak, Claudio Kopper
   and Jakob van Santen. The IceCube collaboration gratefully acknowledge
   the support from the following agencies: USA - U.S. National Science
   Foundation-Office of Polar Programs, U.S. National Science
   Foundation-Physics Division, Wisconsin Alumni Research Foundation,
   Center for High Throughput Computing (CHTC) at the University of
   Wisconsin-Madison, Open Science Grid (OSG), Extreme Science and
   Engineering Discovery Environment (XSEDE), U.S. Department of
   Energy-National Energy Research Scientific Computing Center, Particle
   astrophysics research computing center at the University of Maryland,
   Institute for Cyber-Enabled Research at Michigan State University, and
   Astroparticle physics computational facility at Marquette University;
   Belgium -Funds for Scientific Research (FRS-FNRS and FWO), FWO Odysseus
   and Big Science programmes, and Belgian Federal Science Policy Office
   (Belspo); Germany -Bundesministerium fur Bildung und Forschung (BMBF),
   Deutsche Forschungsgemeinschaft (DFG), Helmholtz Alliance for
   Astroparticle Physics (HAP), Initiative and Networking Fund of the
   Helmholtz Association, Deutsches Elektronen Synchrotron (DESY), and High
   Performance Computing cluster of the RWTH Aachen; Sweden - Swedish
   Research Council, Swedish Polar Research Secretariat, Swedish National
   Infrastructure for Computing (SNIC), and Knut and Alice Wallenberg
   Foundation; Australia - Australian Research Council; Canada - Natural
   Sciences and Engineering Research Council of Canada, Calcul Quebec,
   Compute Ontario, Canada Foundation for Innovation, WestGrid, and Compute
   Canada; Denmark - Villum Fonden, Danish National Research Foundation
   (DNRF), Carlsberg Foundation; New Zealand - Marsden Fund; Japan - Japan
   Society for Promotion of Science (JSPS) and Institute for Global
   Prominent Research (IGPR) of Chiba University; Korea -National Research
   Foundation of Korea (NRF); Switzerland -Swiss National Science
   Foundation (SNSF). Others: We thank the anonymous referee for useful
   comments. EK, SJS and KS acknowledge support from the Science and
   Technology Facilities Council (STFC; ST/P000312/1, ST/N002520/1). SJS
   acknowledges funding from the European Research Council under the
   European Union's Seventh Framework Programme (FP7/2007-2013)/ERC Grant
   agreement no {[}291222].; r TWC acknowledgments the funding provided by
   the Alexander von Humboldt Foundation. AF thanks Irene Tamborra for
   fruitful discussions on neutrino production in supernovae. AF is
   supported by the Initiative and Networking Fund of the Helmholtz
   Association. This work is based (in part) on observations collected at
   the European Organisation for Astronomical Research in the Southern
   Hemisphere, Chile as part of PESSTO, (the Public ESO Spectroscopic
   Survey for Transient Objects Survey) ESO program 188. D-3003 and the DDT
   programme 297. D-5024. Based on observations obtained at the Gemini
   Observatory, which is operated by the Association of Universities for
   Research in Astronomy, Inc., under a cooperative agreement with the NSF
   on behalf of the Gemini partnership: the National Science Foundation
   (United States), the National Research Council (Canada), CONICYT
   (Chile), Ministerio de Ciencia, Tecnologia e Innovacion Productiva
   (Argentina), and Ministerio da Ciencia, Tecnologia e Inovacao (Brazil).
   Observations were carried out under programme GN-2016A-DD-9. Based on
   observations obtained with MegaPrime/MegaCam, a joint project of CFHT
   and CEA/IRFU, at the Canada-France-Hawaii Telescope (CFHT) which is
   operated by the National Research Council (NRC) of Canada, the Institut
   National des Science de l'Univers of the Centre National de la Recherche
   Scientifique (CNRS) of France, and the University of Hawaii. This work
   is based in part on data products produced at Terapix available at the
   Canadian Astronomy Data Centre as part of the CanadaFrance-Hawaii
   Telescope Legacy Survey, a collaborative project of NRC and CNRS. We
   have made use of the Weizmann interactive supernova data repository -
   (http://wiserep.weizmann.ac.il).This research has made use of the
   NASA/IPAC Extragalactic Database (NED) which is operated by the Jet
   Propulsion Laboratory, California Institute of Technology, under
   contract with the National Aeronautics and Space Administration. Funding
   for SDSS-III has been provided by the Alfred P. Sloan Foundation, the
   Participating Institutions, the National Science Foundation, and the
   U.S. Department of Energy O ffi ce of Science. The SDSS-III web site is
   (http://www.sdss3.org/). SDSS-III is managed by the Astrophysical
   Research Consortium for the Participating Institutions of the SDSS-III
   Collaboration including the University of Arizona, the Brazilian
   Participation Group, Brookhaven National Laboratory, Carnegie Mellon
   University, University of Florida, the French Participation Group, the
   German Participation Group, Harvard University, the Instituto de
   Astrofisica de Canarias, the Michigan State/Notre Dame/JINA
   Participation Group, Johns Hopkins University, Lawrence Berkeley
   National Laboratory, Max Planck Institute for Astrophysics, Max Planck
   Institute for Extraterrestrial Physics, New Mexico State University, New
   York University, Ohio State University, Pennsylvania State University,
   University of Portsmouth, Princeton University, the Spanish
   Participation Group, University of Tokyo, University of Utah, Vanderbilt
   University, University of Virginia, University of Washington, and Yale
   University.},
Number-of-Cited-References = {120},
Times-Cited = {12},
Usage-Count-Last-180-days = {1},
Usage-Count-Since-2013 = {10},
Journal-ISO = {Astron. Astrophys.},
Doc-Delivery-Number = {IE7ZQ},
Web-of-Science-Index = {Science Citation Index Expanded (SCI-EXPANDED)},
Unique-ID = {WOS:000472594000001},
OA = {Green Published, Green Submitted, Bronze},
DA = {2024-01-15},
}
